Jose Antonio Escudero

Fitness cost and interference of Arm/Rmt aminoglycoside resistance with the RsmF housekeeping methyltransferases.

ABSTRACT Arm/Rmt methyltransferases have emerged recently in pathogenic bacteria as enzymes that confer high-level resistance to 4,6-disubstituted aminoglycosides through methylation of the G1405 residue in the 16S rRNA (like ArmA and RmtA to -E). In prokaryotes, nucleotide methylations are the most common type of rRNA modification, and they are introduced posttranscriptionally by a variety of site-specific housekeeping enzymes to optimize ribosomal function. Here we show that while the aminoglycoside resistance methyltransferase RmtC methylates G1405, it impedes methylation of the housekeeping methyltransferase RsmF at position C1407, a nucleotide that, like G1405, forms part of the aminoglycoside binding pocket of the 16S rRNA. To understand the origin and consequences of this phenomenon, we constructed a series of in-frame knockout and knock-in mutants of Escherichia coli, corresponding to the genotypes rsmF+, ΔrsmF, rsmF+ rmtC+, and ΔrsmF rmtC+. When analyzed for the antimicrobial resistance pattern, the ΔrsmF bacteria had a decreased susceptibility to aminoglycosides, including 4,6- and 4,5-deoxystreptamine aminoglycosides, showing that the housekeeping methylation at C1407 is involved in intrinsic aminoglycoside susceptibility in E. coli. Competition experiments between the isogenic E. coli strains showed that, contrary to expectation, acquisition of rmtC does not entail a fitness cost for the bacterium. Finally, matrix-assisted laser desorption ionization (MALDI) mass spectrometry allowed us to determine that RmtC methylates the G1405 residue not only in presence but also in the absence of aminoglycoside antibiotics. Thus, the coupling between housekeeping and acquired methyltransferases subverts the methylation architecture of the 16S rRNA but elicits Arm/Rmt methyltransferases to be selected and retained, posing an important threat to the usefulness of aminoglycosides worldwide.

Fluoroquinolone Efflux in Streptococcus suis Is Mediated by SatAB and Not by SmrA

ABSTRACT Streptococcus suis is an emerging zoonotic pathogen. With the lack of an effective vaccine, antibiotics remain the main tool to fight infections caused by this pathogen. We have previously observed a reserpine-sensitive fluoroquinolone (FQ) efflux phenotype in this species. Here, SatAB and SmrA, two pumps belonging to the ATP binding cassette (ABC) and the major facilitator superfamily (MFS), respectively, have been analyzed in the fluoroquinolone-resistant clinical isolate BB1013. Genes encoding these pumps were overexpressed either constitutively or in the presence of ciprofloxacin in this strain. These genes could not be cloned in plasmids in Escherichia coli despite strong expression repression. Finally, site-directed insertion of smrA and satAB in the amy locus of the Bacillus subtilis chromosome using ligated PCR amplicons allowed for the functional expression and study of both pumps. Results showed that SatAB is a narrow-spectrum fluoroquinolone exporter (norfloxacin and ciprofloxacin), susceptible to reserpine, whereas SmrA was not involved in fluoroquinolone resistance. Chromosomal integration in Bacillus is a novel method for studying efflux pumps from Gram-positive bacteria, which enabled us to demonstrate the possible role of SatAB, and not SmrA, in fluoroquinolone efflux in S. suis.

ArmA Methyltransferase in a Monophasic Salmonella enterica Isolate from Food

ABSTRACT The 16S rRNA methyltransferase ArmA is a worldwide emerging determinant that confers high-level resistance to most clinically relevant aminoglycosides. We report here the identification and characterization of a multidrug-resistant Salmonella enterica subspecies I.4,12:i:− isolate recovered from chicken meat sampled in a supermarket on February 2009 in La Reunion, a French island in the Indian Ocean. Susceptibility testing showed an unusually high-level resistance to gentamicin, as well as to ampicillin, expanded-spectrum cephalosporins and amoxicillin-clavulanate. Molecular analysis of the 16S rRNA methyltransferases revealed presence of the armA gene, together with blaTEM-1, blaCMY-2, and blaCTX-M-3. All of these genes could be transferred en bloc through conjugation into Escherichia coli at a frequency of 10−5 CFU/donor. Replicon typing and S1 pulsed-field gel electrophoresis revealed that the armA gene was borne on an ∼150-kb broad-host-range IncP plasmid, pB1010. To elucidate how armA had integrated in pB1010, a PCR mapping strategy was developed for Tn1548, the genetic platform for armA. The gene was embedded in a Tn1548-like structure, albeit with a deletion of the macrolide resistance genes, and an IS26 was inserted within the mel gene. To our knowledge, this is the first report of ArmA methyltransferase in food, showing a novel route of transmission for this resistance determinant. Further surveillance in food-borne bacteria will be crucial to determine the role of food in the spread of 16S rRNA methyltransferase genes worldwide.

Contribution of ROB-1 and PBP3 mutations to the resistance phenotype of a β-lactamase-positive amoxicillin/clavulanic acid-resistant Haemophilus influenzae carrying plasmid pB1000 in Italy

OBJECTIVESnplasmid pB1000 bearing bla(ROB-1) is responsible for high-level β-lactam resistance in Haemophilus influenzae as well as in Pasteurella multocida and Haemophilus parasuis isolates from Spain. Here, we explore the presence of ROB-1 in Italy and investigate the relative contribution of penicillin-binding protein 3 (PBP3) mutations and ROB-1 to the β-lactam resistance phenotype in H. influenzae.nnnMETHODSnthe collection of the Italian Reference Laboratory of H. influenzae was investigated for ROB-1-positive isolates between 2004 and 2009. H. influenzae Rd KW20 was used as recipient for pB1000 electroporation and for mutagenesis of the ftsI gene encoding PBP3.nnnRESULTSnthe presence of plasmid pB1000 in a non-typeable H. influenzae isolated in Italy, BB1059, is reported in this work. This strain is not genetically related to the H. influenzae clinical isolates bearing pB1000 described in Spain. The sequence of ftsI from BB1059 revealed several mutations in the predicted amino acid sequence of PBP3. To determine the relative contribution of pB1000 and PBP3 mutations to the β-lactam resistance phenotype of BB1059, H. influenzae Rd KW20 was transformed with ftsI and/or pB1000 from BB1059. β-Lactam resistance profiles revealed the additive effect of pB1000 and PBP3 mutations conferring resistance to β-lactams, including amoxicillin/clavulanic acid and third-generation cephalosporins.nnnCONCLUSIONSnintra-European spread of plasmid pB1000 among H. influenzae has been shown. The coexistence of plasmid pB1000 and mutations in PBP3 produces an additive resistance phenotype in H. influenzae.

Novel genetic environment of qnrB2 associated with TEM-1 and SHV-12 on pB1004, an IncHI2 plasmid, in Salmonella Bredeney BB1047 from Spain.

The presence of the qnrB2 gene in animal isolates and zoo-notic pathogens opens the possibility that genetic exchange and plasmid acquisition of the qnrB2 gene could occur in the faecal flora of the animals. Interestingly, p137.25 belongs to the IncN plasmid family that is able to replicate in different enterobacter-ial strains, but also seems prevalent in faecal flora from animals. In fact, a study performed on a large collection of E. coli from the USA demonstrated that the prevalence of IncN plasmids is high in avian E. coli (10% – 16%) but negative in E. coli from faeces of healthy humans. 15 This evidence supports the hypothesis that the Salmonella 137.25 strain acquired the qnrB2 gene on an IncN plasmid circulating in avian bacterial flora. This strain could cause infections in humans through the food chain and the resistance plasmid contributes to the dissemination of the qnrB2 gene in other Enterobacteriaceae. None to declare.

First identification of Salmonella Urbana and Salmonella Ouakam in humans in Africa.

INTRODUCTIONnSalmonella infections are increasing worldwide, but there are few reports on Salmonella surveillance in African countries and other developing countries. This has made it difficult to estimate the actual burden of salmonellosis, especially in Africa. This study was conducted in a neglected Northern Region of Ghana where there are no previous data on Salmonella serotypes.nnnMETHODOLOGYnStandard microbiological tests were used for isolation, identification, and serotyping. Micro-dilution was used for the antimicrobial susceptibility tests.nnnRESULTSnFour serotypes of Salmonella were identified: S. Urbana, S. Ouakam, S. Senftenberg, and S. Stanleyville. All the serotypes were susceptible to the 20 antibiotics used in the susceptibility test. S. Urbana and S. Ouakam were identified in humans for the first time in Africa.nnnCONCLUSIONnThis study may serve as a baseline study for future investigations on Salmonella in the region and may assist public health officials to take the appropriate measures in case of a disease outbreak caused by Salmonella in the area. The article may also give health officials a fair idea of the resistance level of these serotypes in the region.

Culturable aerobic and facultative bacteria from the gut of the polyphagic dung beetle Thorectes lusitanicus

Unlike other dung beetles, the Iberian geotrupid, Thorectes lusitanicus, exhibits polyphagous behavior; for example, it is able to eat acorns, fungi, fruits, and carrion in addition to the dung of different mammals. This adaptation to digest a wider diet has physiological and developmental advantages and requires key changes in the composition and diversity of the beetles gut microbiota. In this study, we isolated aerobic, facultative anaerobic, and aerotolerant microbiota amenable to grow in culture from the gut contents of T. lusitanicus and resolved isolate identity to the species level by sequencing 16S rRNA gene fragments. Using BLAST similarity searches and maximum likelihood phylogenetic analyses, we were able to reveal that the analyzed fraction (culturable, aerobic, facultative anaerobic, and aerotolerant) of beetle gut microbiota is dominated by the phyla Proteobacteria, Firmicutes, and Actinobacteria. Among Proteobacteria, members of the order Enterobacteriales (Gammaproteobacteria) were the most abundant. The main functions associated with the bacteria found in the gut of T. lusitanicus would likely include nitrogen fixation, denitrification, detoxification, and diverse defensive roles against pathogens.

SatR Is a Repressor of Fluoroquinolone Efflux Pump SatAB

ABSTRACT Streptococcus suis is an emerging zoonotic agent responsible for high-mortality outbreaks among the human population in China. In this species, the ABC transporter SatAB mediates fluoroquinolone resistance when overexpressed. Here, we describe and characterize satR, an open reading frame (ORF) encoding a MarR superfamily regulator that acts as a repressor of satAB. satR is cotranscribed with satAB, and its interruption entails the overexpression of the pump, leading to a clinically relevant increase in resistance to fluoroquinolones.

Highly Tigecycline-Resistant Klebsiella pneumoniae Sequence Type 11 (ST11) and ST147 Isolates from Companion Animals

ABSTRACT In this study, we characterized two tigecycline-resistant Klebsiella pneumoniae isolates from dog urine samples. The isolates were genetically unrelated, belonging to sequence type 11 (ST11) and ST147, both classically related to human isolates. To the best of our knowledge, this is the first identification of tigecycline-resistant isolates from animals. We unveil here the worrisome circulation among animals of bacterial clones resistant to this last-resort antibiotic.

Multicopy plasmids allow bacteria to escape from fitness trade-offs during evolutionary innovation

Understanding the mechanisms governing innovation is a central element of evolutionary theory. Novel traits usually arise through mutations in existing genes, but trade-offs between new and ancestral protein functions are pervasive and constrain the evolution of innovation. Classical models posit that evolutionary innovation circumvents the constraints imposed by trade-offs through genetic amplifications, which provide functional redundancy. Bacterial multicopy plasmids provide a paradigmatic example of genetic amplification, yet their role in evolutionary innovation remains largely unexplored. Here, we reconstructed the evolution of a new trait encoded in a multicopy plasmid using TEM-1 β-lactamase as a model system. Through a combination of theory and experimentation, we show that multicopy plasmids promote the coexistence of ancestral and novel traits for dozens of generations, allowing bacteria to escape the evolutionary constraints imposed by trade-offs. Our results suggest that multicopy plasmids are excellent platforms for evolutionary innovation, contributing to explain their extreme abundance in bacteria.Trade-offs are common during evolutionary innovation. Here, the authors show that multicopy plasmids allow coexistence of the ancestral and evolved alleles in the TEM-1 β-lactamase system, helping bacteria to escape evolutionary constraints imposed by trade-offs.