Prevalence of colistin resistance in Escherichia coli: mcr-1-positive clinical isolates in Lombardy, Northern Italy
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Abstract
Background: The recent emergence of the plasmid-mediated colistin resistance mechanism in
Escherichia coli, Klebsiella pneumoniae and Salmonella spp. has raised concern among public health
experts as colistin is a last-line antibiotic for the treatment of infections by carbapenem resistant
Enterobacteriaceae. The aim of the study was to investigate i) the prevalence of this resistance trait in
E. coli, and ii) the presence of mcr-1 and mcr-2 genes among colistin-resistant isolates in the
Lombardy region, Northern Italy.
Material/methods: The study was performed during a 4-month period (May-August 2016) in six acute
care Hospitals. Non duplicated E. coli isolates from clinical samples of both outpatients and inpatients
were included in the study (surveillance rectal swabs were excluded). Bacterial species identification
was obtained by MALDI-TOF mass spectrometry. Colistin resistance (MIC > 2 mg/L) was first
evaluated by routine automated systems and then confirmed by the reference broth microdilution
method (EUCAST, 2016). Amplification of mcr-type genes, and microarray analysis were
accomplished. Phylogroup identification, rep-PCR (DiversiLab) and PFGE (XbaI) were used for
genotyping. The mcr-1-positive plasmids were characterized by PBRT kit and PCR (IncX).
Results: Overall, 3902 E. coli isolates were evaluated (1560 from inpatients, 2342 from outpatients).
Of them, 18/3902 (0.5%), collected from 4/6 centers, showed resistance to colistin. These isolates
were obtained from both inpatients (n=6) and outpatients (n=12). In particular, hospitalized patients
were from medical (3/6), rehabilitation (2/6), and surgical (1/6) wards. The great majority of colistinresistant
isolates were from urine (16/18) but two of them were from blood cultures. Colistin MIC
values ranged from 4 to 16 mg/L (as assessed by the reference method). The mcr-1 gene was
detected in 10/18 isolates, all of which from urine cultures (7 from outpatients, 3 from inpatients). In
these cases, colistin MIC values ranged from 4 to 8 mg/L. Of note, 6/10 mcr-1-positive E. coli isolates
were also resistant to ciprofloxacin and trimethoprim-sulfamethoxazole, and 2 of them were also
positive for the SHV-12 ESBL enzyme. All mcr-1-positive E. coli strains resulted unrelated by PFGE
analysis, while rep-PCR showed eight different clusters. The identified phylogroups were A and D (in
four cases each), B1 and B2 (in one case each). The incompatibility groups were IncX4 in 7/10 strains,
IncHI2 in the remaining 3/10. The mcr-2 gene was never detected.
Conclusions: According to most recent surveillances, our study demonstrates a low prevalence of
colistin resistance among E. coli isolates also in the Lombardy region. In addition, our data show that
the mcr-1 gene plays a prominent role in this context. Of particular concern, it appears the frequent
detection of mcr-1 gene among isolates from urine cultures of outpatients, thus suggesting the
opportunity of routine testing the antimicrobial susceptibility for colistin in these cases