Co-occurrence of genes encoding carbapenemase, ESBL, pAmpC and non-β-Lactam resistance among Klebsiella pneumonia and E. coli clinical isolates in Tunisia

Abstract

This study aimed to investigate the molecular mechanisms of carbapenem and colistin resistance in K. pneumoniae and E. coli isolates obtained from hospitalized patients in Carthagene International Hospital of Tunis. A total of 25 K. pneumoniae and 2 E. coli clinical isolates with reduced susceptibility to carbapenems were recovered. Susceptibility testing and phenotypic screening tests were carried out. ESBL, AmpC, carbapenemase and other antibiotic resistance genes were sought by PCR‐sequencing. The presence of plasmid‐mediated colistin resistance genes (mcr‐1‐8) was examined by PCR and the nucleotide sequence of the mgrB gene was determined. The analysis of plasmid content was performed by PCR‐Based Replicon Typing (PBRT). The clonality of isolates was assessed by PFGE and multilocus sequence typing (MLST). All of the isolates produced carbapenemase activity. They showed a great variation in the distribution of ESBL, AmpC, carbapenemase and other plasmid‐mediated resistance determinants. K. pneumoniae isolates carried blaNDM‐1 (n = 11), blaOXA‐48 (n = 11), blaNDM‐1 + blaOXA‐48 (n = 1), blaNDM‐1 + blaVIM‐1 (n = 1), blaOXA‐204 (n = 1), along with blaCTX‐M, blaOXA, blaTEM, blaCMY, blaDHA and blaSHV genes variants on conjugative plasmid of IncL/M, IncR, IncFIIK, IncFIB, and IncHI1 types. Three sequence types ST101, ST307 and ST15 were identified. The mgrB alteration g109a (G37S) was detected in a single colistin‐resistant, NDM‐1 and OXA‐48‐coproducing K. pneumoniae isolate. The two E. coli isolates belonged to ST95, co‐produced NDM‐1 and CTX‐M‐15, and harboured plasmid of IncFII and IncFIB types. To our knowledge, this is the first report in Tunisia of NDM‐1, OXA‐48, and CTX‐M‐15 coexistence in colistin‐resistant K. pneumoniae ST15.

Genetic heterogeneity and predominance of blaCTX-M-15 in cefotaxime-resistant Enterobacteriaceae isolates colonizing hospitalized children in Tunisia

“…Interestingly, K. pneumoniae ST101 is one of the major high-risk clonal lineages of carbapanemase-producing isolates highly associated with hospital-acquired infections worldwide (David et al 2019). In Tunisia, the ST101 was recently reported in CTX-M-15and OXA-48-producing K. pneumoniae in hospital settings and communities (Mansour et al 2015;Ben Tanfous et al 2017Ben Sallem et al 2022). Similarly, carbapenemase-producing K. pneumoniae ST13 and ST37 clones have been reported as prevalent clones in various geographic regions, such as Portugal (Mendes et al 2022), Brazil (Rodrigues et al 2022) and Italy (Di Pilato et al 2021).…”

“…2017, 2018; Ben Sallem et al . 2022). Similarly, carbapenemase‐producing K. pneumoniae ST13 and ST37 clones have been reported as prevalent clones in various geographic regions, such as Portugal (Mendes et al .…”

Screening and Characterization of Multidrug-Resistant Enterobacterales among Hospitalized Patients in the African Archipelago of Cape Verde

“…In the African continent, besides South Africa, ST307 was found to be predominant among ESBL-producing K. pneumoniae isolated between 2016 and 2018 from three sentinel surveillance hospitals in Nigeria [ 22 ]. In addition, a K. pneumoniae ST307 clinical isolate harboring the bla OXA-48 gene on an IncL-type plasmid was reported in Tunisia in the same period [ 23 ]. Of note, genome sequencing identified ST307 among chimpanzees and termites in protected areas in Senegal, suggesting the circulation of strains between the two species [ 24 ].…”

“…None of the isolates were resistant to the newly developed ceftazidime/avibactam combination. pneumoniae ST307 clinical isolate harboring the blaOXA-48 gene on an IncL-type plasmid was reported in Tunisia in the same period [23]. Of note, genome sequencing identified ST307 among chimpanzees and termites in protected areas in Senegal, suggesting the circulation of strains between the two species [24].…”

Phenotypic Characterization of Carbapenemase-Producing Enterobacteriaceae Strains in a Referral Teaching Hospital in Yaoundé, Cameroon

“…In Tunisia, Sallem et al showed wide variation in the distribution of ESBLs, AmpC, carbapenemase and other plasmid-mediated resistance determinants. Isolates of Klebsiella pneumoniae producing carbapenemase activity carried variants of the blaNDM-1 (n = 11), blaOXA-48 (n = 11), blaNDM-1 + blaOXA-48 (n = 1), blaNDM-1 + blaVIM-1 (n = 1), blaOXA-204 (n = 1), as well as variants of the blaCTX-M, blaOXA, bla-TEM, blaCMY, blaDHA and blaSHV genes on conjugative plasmid [30]. This could be explained by the fact that, Klebsiella easily host carbapenemases genes.…”