We report a high prevalence of MCR-1 and CTX-M-1-producing Escherichia coli in three Tunisian chicken farms. Chickens were imported from France or derived from French imported chicks. The same IncHI2-type plasmid reported to carry those genes in cattle in France and in a food sample in Portugal was found in Tunisian chickens of French origin. This suggests a significant impact of food animal trade on the spread of mcr-1-mediated colistin resistance in Europe.

The emergence of colistin-resistant Klebsiella pneumoniae (CoR Kp ) is a public health concern, since this antibiotic has become the last line of treatment for infections caused by multidrug-resistant (MDR) Gram negatives. In this study, we have investigated the molecular basis of colistin resistance in 13 MDR K. pneumoniae strains isolated from 12 patients in a teaching hospital in Sousse, Tunisia. Whole-genome sequencing (WGS) was used to decipher the molecular mechanism of colistin resistance and to identify the resistome of these CoR Kp isolates. It revealed a genome of ca. 5.5 Mbp in size with a G+C content of 57%, corresponding to that commonly observed for K. pneumoniae . These isolates belonged to the 5 different sequence types (ST11, ST15, ST101, ST147, and ST392), and their resistome was composed of acquired β-lactamases, including extended-spectrum beta-lactamase and carbapenemase genes ( bla _CTX-M-15 , bla _OXA-204 , bla _OXA-48 , and bla _NDM-1 genes), aminoglycoside resistance genes [ aac ( 6 ′) Ib-cr , aph ( 3 ″)- Ib , aph ( 6 )- Id , and aac ( 3 )- IIa ], and fosfomycin ( fosA ), fluoroquinolone ( qnr -like), chloramphenicol, trimethoprim, and tetracycline resistance genes. All of the isolates were identified as having a mutated mgrB gene. Mapping reads with reference sequences of the most common genes involved in colistin resistance revealed several modifications in mgrB , pmr , and pho operons (deletions, insertions, and substitutions) likely affecting the function of these proteins. It is worth noting that among the 12 patients, 10 were treated with colistin before the isolation of CoR Kp . No plasmid encoding mcr-1 to mcr-5 genes was found in these isolates. This study corresponds to the first molecular characterization of a collection of CoR Kp strains in Tunisia and highlights that the small-transmembrane protein MgrB is a main mechanism for colistin resistance in K. pneumoniae .

The spread of plasmid-mediated quinolone resistance determinants (qnr-like determinants, aac(6')-Ib-cr and qepA genes) was evaluated in a collection of 281 nalidixic acid-resistant enterobacterial isolates recovered between September 2005 and December 2007 at the Sahloul Hospital, Sousse, Tunisia. Sixteen percent of those isolates carried qnr genes encoding the QnrB1, QnrB2, QnrA6 or QnrS1 determinants. Most qnr-positive isolates were extended-spectrum ß-lactamase (ESBL) producers, being predominantly of the CTX-M-15 type, but also of the SHV-28 and SHV-12 types. The qnr genes were located on plasmids with a size in the range 55-150 kb. The qnrB2 gene was associated with sul1-type integron structures and the qnrB1 gene was associated with orf1005, whereas the genetic environment of qnrA6 was unknown. In two isolates, the qnrS1 gene was located downstream of an ISEcl2 element on plasmids that often carried the narrow-spectrum ß-lactamase gene bla(LAP-2); qepA and aac(6')-Ib-cr were not detected. The present study highlights the wide spread of Qnr-like determinants in Tunisia, with an association with the ESBL CTX-M-15 in human clinical isolates.

The basis of the beta-lactam resistance of 39 multidrug-resistant Acinetobacter baumannii isolates recovered from hospitalized patients was studied. These isolates were collected from 2001 to 2005 at the Sahloul Hospital in Sousse, Tunisia. They belonged to two distinct clones. One clone that grouped 19 isolates produced a carbapenem-hydrolyzing oxacillinase, OXA-97, that differed from OXA-58 by a single amino acid substitution and conferred the same beta-lactam resistance profile as OYA-58. The bla(OXA-97) gene was located on plasmids that varied in size in 18 isolates and was chromosomally located in a single isolate. Cloning and sequencing identified genetic structures surrounding the bla(OXA-97) gene similar to those reported to be adjacent to the bla(OXA-58) gene. In addition, the novel ISAba8 element (which is of the IS21 family) was identified. This is the first report of the nosocomial spread of carbapenemase producers in A. baumannii isolates in Africa.

One hundred extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae were recovered from the intensive care unit and the urology ward of the University Hospital of Sahloul in Tunisia between May 2005 and May 2006. The majority of strains showed a high level of resistance to cefotaxime and ceftazidime. Double-disk synergy test and E-test strips were used to confirm production of ESBLs. The molecular analysis revealed that the majority of strains (91%) carried genes encoding CTX-M-15. SHV-12 and SHV-2a were produced, respectively, by 9% and 3% of the strains. Pulsed-field gel electrophoresis of ESBL-producing Klebsiella pneumoniae isolates revealed four different clonal groups and three for Escherichia coli , showing the absence of spread of any epidemic clone. The CTX-M-15 ESBL-producing E. coli of the major clonal group belong to the B2 phylogenetic group, to the sequence type 131, and has a high virulence potential. In conclusion, CTX-M-15 ESBLs accounted for the overwhelming majority of ESBL types among Enterobacteriaceae from our hospital. This study confirms the high rate of ESBLs in Tunisia and further demonstrates the worldwide spread of genes coding for CTX-M-15 enzymes in clinical isolates.