Characterization of ESBL-Producing <i>Escherichia coli</i> and <i>Klebsiella pneumoniae</i> Isolated from Clinical Samples in a Northern Portuguese Hospital: Predominance of CTX-M-15 and High Genetic Diversity

• Main Authors: Isabel Carvalho, José António Carvalho, Sandra Martínez-Álvarez, Madjid Sadi, Rosa Capita, Carlos Alonso-Calleja, Fazle Rabbi, Maria de Lurdes Nunes Enes Dapkevicius, Gilberto Igrejas, Carmen Torres, Patrícia Poeta
• Format: Article
• Language: English
• Published: MDPI AG 2021-09-01
• Series: Microorganisms
• Subjects: antimicrobial resistance; <i>Klebsiella pneumoniae</i>; <i>Escherichia coli</i>; public health; Carbapenemases; β-lactamases
• Online Access: https://www.mdpi.com/2076-2607/9/9/1914

Background: <i>Enterobacteriaceae</i> are major players in the spread of resistance to β-lactam antibiotics through the action of CTX-M β-lactamases. We aimed to analyze the diversity and genetic characteristics of ESBL-producing <i>Escherichia coli</i> and <i>Klebsiella pneumoniae</i> isolates from patients in a Northern Portuguese hospital. Methods: A total of 62 cefotaxime/ceftazidime-resistant <i>E. coli</i> (<i>n</i> = 38) and <i>K. pneumoniae</i> (<i>n</i> = 24) clinical isolates were studied. Identification was performed by MALDI-TOF MS. Antimicrobial susceptibility testing against 13 antibiotics was performed. Detection of ESBL-encoding genes and other resistance genes, phylogenetic grouping, and molecular typing (for selected isolates) was carried out by PCR/sequencing. Results: ESBL activity was detected in all 62 <i>E. coli</i> and <i>K. pneumoniae</i> isolates. Most of the ESBL-producing <i>E. coli</i> isolates carried a <i>bla</i>_CTX-M gene (37/38 isolates), being <i>bla</i>_CTX-M-15 predominant (<i>n</i> = 32), although <i>bla</i>_CTX-M-27 (<i>n</i> = 1) and <i>bla</i>_CTX-M-1 (<i>n</i> = 1) were also detected. Two <i>E. coli</i> isolates carried the <i>bla</i>_KPC2/3 gene. The lineages ST131-B2 and ST410-A were detected among the ESBL-producing blood <i>E. coli</i> isolates. Regarding the 24 ESBL-producing <i>K. pneumoniae</i> isolates, 18 carried a <i>bla</i>_CTX-M gene (<i>bla</i>_CTX-M-15, 16 isolates; <i>bla</i>_CTX-M-55, 2 isolates). All <i>K. pneumoniae</i> isolates carried <i>bla</i>_SHV genes, including ESBL-variants (<i>bla</i>_SHV-12 and <i>bla</i>_SHV-27, 14 isolates) or non-ESBL-variants (<i>bla</i>_SHV-11 and <i>bla</i>_SHV-28, 10 isolates); ten <i>K. pneumoniae</i> isolates also carried the <i>bla</i>_KPC2/3 gene and showed imipenem-resistance. ESBL-positive <i>E. coli</i> isolates were ascribed to the B₂ phylogenetic group (82%), mostly associated with ST131 lineage and, at a lower rate, to ST410/A. Regarding <i>K. pneumoniae</i>, the three international lineages ST15, ST147, and ST280 were detected among selected isolates. Conclusions: Different ESBL variants of CTX-M (especially CTX-M-15) and SHV-type (specially SHV-12) were detected among CTX/CAZ^R<i>E. coli</i> and <i>K. pneumoniae</i> isolates, in occasions associated with carbapenemase genes (<i>bla</i>_KPC2/3 gene).