A Study in a Regional Hospital of a Mid-Sized Spanish City Indicates a Major Increase in Infection/Colonization by Carbapenem-Resistant Bacteria, Coinciding with the COVID-19 Pandemic
Bacterial resistance to antibiotics has proven difficult to control over the past few decades.
The large group of multidrug-resistant bacteria includes carbapenemase-producing bacteria (CPB),
for which limited therapeutic options and infection control measures are available. Furthermore,
carbapenemases associate with high-risk clones that are defined by the sequence type (ST) to which
each bacterium belongs. The objectives of this cross-sectional and retrospective study were to
describe the CPB population isolated in a third-level hospital in Southern Spain between 2015 and
2020 and to establish the relationship between the ST and the epidemiological situation defined by
the hospital. CPB were microbiologically studied in all rectal and pharyngeal swabs and clinical
samples received between January 2015 and December 2020, characterizing isolates using MicroScan
and mass spectrometry. Carbapenemases were detected by PCR and Sanger sequencing, and STs
were assigned by multilocus sequence typing (MLST). Isolates were genetically related by pulsedfield gel electrophoresis using Xbal, Spel, or Apal enzymes. The episodes in which each CPB was
isolated were recorded and classified as involved or non-involved in an outbreak. There were
320 episodes with CPB during the study period: 18 with K. pneumoniae, 14 with Klebisella oxytoca,
9 with Citrobacter freundii, 11 with Escherichia coli, 46 with Enterobacter cloacae, 70 with Acinetobacter
baumannii, and 52 with Pseudomonas aeruginosa. The carbapenemase groups detected were OXA, VIM,
KPC, and NDM with various subgroups. Synchronous relationships were notified between episodes
of K. pneumoniae and outbreaks for ST15, ST258, ST307, and ST45, but not for the other CPB. There
was a major increase in infections with CPB over the years, most notably during 2020, coinciding
with the COVID-19 pandemic. This study highlights the usefulness of gene sequencing techniques to
control the spread of these microorganisms, especially in healthcare centers. These techniques offer
faster results, and a reduction in their cost may make their real-time application more feasible. The
combination of epidemiological data with real-time molecular sequencing techniques can provide a
major advance in the transmission control of these CPB and in the management of infected patients.
Real-time sequencing is essential to increase precision and thereby control outbreaks and target
infection prevention measures in a more effective manner