Emerging Antibiotic Resistances

Patrice Nordmann has joined the University of Fribourg in July 2013. The research interest of P. Nordmann and his group focuses on Emerging Antibiotic Resistances.

Antibiotic resistance is a mutltifaceted problem and truly a global challenge. Its spread worldwide may change significantly human medicine in the next years. As an example, more than 25,000 people die each year due to antibiotic-resistant bacteria in Europe. Emergence of pandrug bacteria and spread of even multidrug-resistant E. coli in the community (outside the hospitals) are among the latest development of this phenomenon. The emergence of such resistance traits are leading to impossible-to-treat infections and difficulties for prevention of infections (immunosuppressed patients, important surgery, transplantation).

Research on antibiotic resistance may be directed for achieving several goals; (i) an increase in the knowledge on the origin, the plasticity and diffusion of resistance genes, (ii) the prevention of their spread by implementing novel diagnostic tools, and (iii) the discovery of novel antibiotic molecules.

Our research is at the frontier between basic Science (Molecular Microbiology) and applied Science (Clinical Microbiology). It gathers mostly two complementary approaches:

• Genetic and biochemical analysis of antibiotic resistance traits which are emerging worldwide.
• Development of diagnostic techniques for rapid identification of emerging antibiotic resistance traits and evaluation of novel antibiotic resistance molecules.

Main lines of research

• Genetic and biochemistry

  Diffusion of antibiotic resistance of worldwide origin is reported currently in distantly-located areas. This is related to globalization of the world, increasing number of travels, and hospitalization of patients abroad. Therefore, we have established an informal worldwide-located network aimed to identify the emerging mechanisms of resistance. Biochemical and genetic analyses have been conducted with clinical isolates that have been first screened according to their multidrug resistance pattern results using phenotypic-based antibiotic susceptibility testing. Special focus has been made on Gram-negative bacterial species that are clinically relevant such as Enterobacteriaceae (E. coli, K. pneumoniae…), Pseudomonas sp. and Acinetobacter sp. We have identified several resistance determinants which are widespread now worldwide and clinically significant such as the extended-spectrum ß-lactamase CTX-M-15 which hydrolyses ß-lactams including cephalosporins, and the carbapenemases of the OXA-48 type. Carbapenemases are proteins which are able to hydrolyze almost all ß-lactams including the carbapenems. The carbapenemase producers are also resistant to many other non ß-lactam antibiotics. By studying many multidrug resistant isolates from worldwide origin, we have identified that the recent spread of the carbapenemases of the NDM type (New Dehli metallo-ß-lactamase), first identified from South-East Asia, has spread at an alarming rate within the last three years (Figure 1). Genome analysis of one of those multidrug-resistant NDM-1 E. coliisolate led us to identify the diversity of the antibiotic resistance traits which may be selected and gathered within a single bacterial genome (Figures 2A, 2B).

  

  Fig.1 – Worldwide distribution of carbapenemases NDM (2010-2013). Green arrows and green stars indicate spread from the main reservoir located in South-East Asia, whereas red arrows and red stars indicate spread from the secondary reservoir, the Middle-East. 

  We have shown recently that the spread of the NDM-1 gene may have occurred from its reservoir organism first to Acinetobacter baumannii (a rare hospital-acquired pathogen), then to Enterobacteriacae (Figure 2). This result contributes a novel paradigm indicating that Acinetobacter baumannii may play an important role for spreading antibiotic resistance genes among unrelated bacterial species. We are studying factors that may enhance expression (anticancer drug bleomycin since a bleomycin resistance gene is located next to the NDM-1 gene (Figure 2)) and gene plasticity of this resistance gene, as well as novel antibiotic resistance genes and genetic elements we have discovered recently (insertion-sequence like elements).

  

  Fig.2 – A novel model of antibiotic gene transfer. A. baumannii as an intermediate acceptor of antibiotic resistance gene.

   

   

   

• Rapid diagnostic techniques for identification of antibiotic resistance and evaluation of novel antibiotic resistance molecules

  Since very few novel antibiotic molecules will be marketed soon, control of antibiotic resistance is mostly based on the development of diagnostic techniques for identification of emerging antibiotic resistance. Those techniques may help to design screening strategy for a better antibiotic stewardship of infected patients as well as a rapid isolation of colonized patients. We have developed rapid diagnostic tests for identification of the most important resistant determinants which are emerging in Gram negatives, the Carba NP test (carbapenemase detection) and the ESBL NDP test (extended-spectrum ß-lactamase detection). The principle of those tests is based on the detection of acid production resulting from the ß-lactam ring hydrolysis. Carba NP test detects hydrolysis of a carbapenem (Figure 3) whereas the ESBL NDP test detects hydrolysis of an extended-spectrum cephalosporin. Those tests may be used with bacterial colonies but also directly with infected human samples such as blood and urines. Results are obtained in less than 2 h with almost 100% sensitivity and specificity. They can be implemented in any clinical laboratory due to their simplicity and their low cost.

  By collaborating with many labs and several biotechs, we are participating also to the identification of novel antibiotic targets and to the evaluation of the in-vitro and in-vivo antibiotic properties of novel antibiotic molecules both using well-genetically defined bacterial isolates and clinical isolates.

   

  

   

  Fig.3 – The Carba NP test. The principle of the test is based on the detection of acid production resulting from the hydrolysis of ß-lactam ring.