Coping with antibiotic resistance: contributions from genomics

Antibiotic resistance is a public health issue of global dimensions with a significant impact on morbidity, mortality and healthcare-associated costs. The problem has recently been worsened by the steady increase in multiresistant strains and by the restriction of antibiotic discovery and development programs. Recent advances in the field of bacterial genomics will further current knowledge on antibiotic resistance and help to tackle the problem. Bacterial genomics and transcriptomics can inform our understanding of resistance mechanisms, and comparative genomic analysis can provide relevant information on the evolution of resistant strains and on resistance genes and cognate genetic elements. Moreover, bacterial genomics, including functional and structural genomics, is also proving to be instrumental in the identification of new targets, which is a crucial step in new antibiotic discovery programs

Evidence of another anthropic impact on iguana delicatissima from the lesser Antilles: the presence of antibiotic resistant enterobacteria

The improper use of antibiotics by humans may promote the dissemination of resistance in wildlife. The persistence and spread of acquired antibiotic resistance and human-associated bacteria in the environment, while representing a threat to wildlife, can also be exploited as a tool to monitor the extent of human impact, particularly on endangered animal species. Hence, we investigated both the associated enterobacterial species and the presence of acquired resistance traits in the cloacal microbiota of the critically endangered lesser Antillean iguana (Iguana delicatissima), by comparing two separate populations living in similar climatic conditions but exposed to different anthropic pressures. A combination of techniques, including direct plating, DNA sequencing and antimicrobial susceptibility testing allowed us to characterize the dominant enterobacterial populations, the an- tibiotic resistant strains and their profiles. A higher frequency of Escherichia coli was found in the samples from the more anthropized site, where multi-drug resistant strains were also isolated. These results confirm how human-associated bacteria as well as their antibiotic-resistance determinants may be transferred to wildlife, which, in turn, may act as a reservoir of antibiotic resistance

Tracking Acquired Antibiotic Resistance in Commensal Bacteria of Galápagos Land Iguanas: No Man, No Resistance

BACKGROUND: Antibiotic resistance, evolving and spreading among bacterial pathogens, poses a serious threat to human health. Antibiotic use for clinical, veterinary and agricultural practices provides the major selective pressure for emergence and persistence of acquired resistance determinants. However, resistance has also been found in the absence of antibiotic exposure, such as in bacteria from wildlife, raising a question about the mechanisms of emergence and persistence of resistant strains under similar conditions, and the implications for resistance control strategies. Since previous studies yielded some contrasting results, possibly due to differences in the ecological landscapes of the studied wildlife, we further investigated this issue in wildlife from a remote setting of the Galapagos archipelago. METHODOLOGY/PRINCIPAL FINDINGS: Screening for acquired antibiotic resistance was carried out in commensal enterobacteria from Conolophus pallidus, the terrestrial iguana of Isla Santa Fe, where: i) the abiotic conditions ensure to microbes good survival possibilities in the environment; ii) the animal density and their habits favour microbial circulation between individuals; and iii) there is no history of antibiotic exposure and the impact of humans and introduced animal species is minimal except for restricted areas. Results revealed that acquired antibiotic resistance traits were exceedingly rare among bacteria, occurring only as non-dominant strains from an area of minor human impact. CONCLUSIONS/SIGNIFICANCE: Where both the exposure to antibiotics and the anthropic pressure are minimal, acquired antibiotic resistance traits are not normally found in bacteria from wildlife, even if the ecological landscape is highly favourable to bacterial circulation among animals. Monitoring antibiotic resistance in wildlife from remote areas could also be a useful tool to evaluate the impact of anthropic pressure

φBO1E, a newly discovered lytic bacteriophage targeting carbapenemase-producing Klebsiella pneumoniae of the pandemic Clonal Group 258 clade II lineage

The pandemic dissemination of KPC carbapenemase-producing Klebsiella pneumoniae (KPC-KP) represents a major public health problem, given their extensive multidrug resistance profiles and primary role in causing healthcare-Associated infections. This phenomenon has largely been contributed by strains of Clonal Group (CG) 258, mostly of clade II, which in some areas represent the majority of KPC-KP isolates. Here we have characterized a newly discovered lytic Podoviridae, named φBO1E, targeting KPC-KP strains of clade II lineage of CG258. Genomic sequencing revealed that φBO1E belongs to the Kp34virus genus (87% nucleotide identity to vB-KpnP-SU552A). ΦBO1E was stable over a broad pH and temperature range, exhibited strict specificity for K. pneumoniae strains of clade II of CG258, and was unable to establish lysogeny. In a Galleria mellonella infection model, φBO1E was able to protect larvae from death following infection with KPC-KP strains of clade II of CG258, including one colistin resistant strain characterized by a hypermucoviscous phenotype. To our best knowledge φBO1E is the first characterized lytic phage targeting K. pneumoniae strains of this pandemic clonal lineage. As such, it could be of potential interest to develop new agents for treatment of KPC-KP infections and for decolonization of subjects chronically colonized by these resistant superbugs

Un peu de génétique financière

Mallet Jean-Philippe. Un peu de génétique financière. In: Revue d'économie industrielle, vol. 18, 4e trimestre 1981. Genèse et développement de la BIOINDUSTRIE. pp. 293-299

The Urgent Need for Novel Antimicrobial Agents and Strategies to Fight Antibiotic Resistance

Antibiotic resistance in bacterial pathogens has currently reached very high and alarming levels [...

Species diversity, spatial distribution, and virulence associated genes of culturable vibrios in a brackish coastal Mediterranean environment

The Vibrio genus is widespread in marine and brackish environments, and several species are human and animal pathogens of global importance. Vibrios adapt rapidly to many environmental stresses, so that brackish environ- ments can be both a suitable niche and a possible reservoir for them. To test the occurrence of culturable vibrios and their possible correlation with environmental factors in a temperate brackish environment, a 1-year sampling study was performed in three brackish ponds located along the Central Thyrrenian coast in the Macchiatonda Nature Reserve (Santa Marinella, district of Rome, Italy). Molecular methods were used to de- tect Vibrio cholerae, V. parahaemolyticus, and V. vulnificus pathogenicity-associated genes among the Vibrio isolates. Out of 130 Vibrio isolates identified by sequencing a recA fragment, 70 harbored virulence-associated genes including ctx, ace, tcpA, tdh, trh, vvhA, vllY, and toxRS, so confirming the spread of virulence determinants across the environmental isolates. Ecological analysis showed that, although the water temperature is known to be a strong predictor of abundance and distribution of vibrios, its influence accounts for 27 % of the observed variance in the Macchiatonda samples, increas- ing to 40 % when combined with salinity

The Relationship between Salinity and Bacterioplankton in Three Relic Coastal Ponds (Macchiatonda Wetland, Italy)

The great environmental importance of wetlands is linked to the high biodiversity of flora and fauna they support, so that the international Ramsar Convention focused on these areas and highlighted the need to preserve them. The bacterial communities that thrive in these ecosystems play a key role in regulating the local biogeochemical processes and yet their distribution, abundance and dynamics are poorly known. This work is aimed to study the bacterial assemblages over a year long, to contribute to the understanding of the natural processes occurring in wetlands at variable salinity. The knowledge of bacterial groups, species or assemblages can provide a useful bioindicator for conservation and restoration efforts. Macchiatonda Natural Reserve (Santa Severa, Rome, Italy) is a relic ecosystem, once found along the entire Tyrrhenian coast. This wetland encompasses three coastal ponds with different salinity, where both peculiar vegetation and highly diverse migratory and resident avifauna can be found. This ancient system has been scarcely investigated and nothing is known about its microbial community. The molecular metagenomic analyses performed to investigate the salinity/bacterioplankton relationship, highlighted differences in the bacterial structure, between ponds and seasons. Analogous trends in SSCP profiles, Shannon Index, and bacterial composition (16S) were observed in the two saltier ponds, whereas the entire set of results was different for the less salty one. The species diversity in the three ponds varied according the salinity gradient, with the maximum diversity corresponding to a salt concentration range between 20 and 30. At higher and lower salinity, the microbial diversity lowers, according to the “Intermediate Disturbance Hypothesis”