Clonal spread of PER-1 and OXA-23 producing extensively drug resistant Acinetobacter baumannii during an outbreak in a burn intensive care unit in Tunisia

Extensively drug resistant Acinetobacter baumannii (XDR-Ab), has emerged as an important pathogen in several outbreaks. The aim of our study was to investigate the eventual genetic relatedness of XDR-Ab strains recovered from burn patients and environment sites in the largest Tunisian Burn Intensive Care Unit (BICU) and to characterize β-lactamase encoding genes in these strains. Between March 04th, 2019 and April 22nd, 2019 an outbreak of XDR-Ab was suspected. Environmental screening was done. All isolates were screened by simplex PCR for β-lactamase genes. Genetic relatedness was determined by pulsed field gel electrophoresis (PFGE) of ApaI-digested total DNA. During the study period, 21 strains of A. baumannii were isolated in burn patients, mainly in blood culture (n = 7) and central vascular catheter (n = 6). All strains were susceptible to colistin but resistant to imipenem (n = 23), ciprofloxacin (n = 23), amikacin (n = 22), tigecyclin (n = 5) and rifampicin (n = 4). The blaOXA-51-like, blaOXA23, and blaADC genes were present in all strains. These resistance determinants were associated with blaPER-1 in 10 strains. The ISAba1 was inserted upstream of blaOXA-23 in all isolates. PFGE revealed two major clusters A (n = 11) and B (n = 5). This is the first description in Tunisia of clonally related PER-1 producing XDR-Ab in burn patients with probable environmental origin.

Insertion sequences and sequence types profile of clinical isolates of carbapenem-resistant A. baumannii collected across India over four year period

OBJECTIVES

Acinetobacter baumannii emerged as a major nosocomial pathogen responsible for infections. In this study, we report the molecular characterization, association of insertion sequences and sequence types of clinical isolates of carbapenem resistant A. baumannii.

MATERIALS AND METHODS

A total of 763 non-duplicate isolates of A. baumannii received from 8 centres across India during January 2014 to December 2017 were studied. Susceptibility testing was done by Kirby-Bauer method. PCR was performed for detection of extended spectrum β-lactamases, metallo β-lactamases, oxacillinases and ISAba1. Mapping PCR was performed to identify the position of ISAba1 with respect to bla_OXA-23 like and bla_OXA-51 like gene. MLST was performed to identify the sequence type. Whole genome sequencing was done to decipher the genetic arrangement of ISAba1 with bla_OXA-23 like and with bla_OXA-51 like.

RESULTS

All the isolates were resistant to imipenem and meropenem. bla_OXA-23 like was the predominant carbapenemase. All isolates were positive for ISAba1. The common sequence types were ST848, ST451 and ST1305 which belongs to International clone II. Whole genome sequencing showed considerable variation in the insertion site location.

CONCLUSIONS

In conclusion, high prevalence of bla_OXA-23 like in A. baumannii and its association with ISAba1 and sequence types belonging to IC-II facilitates the successful dissemination of these extremely drug resistant strains.

Current strategy for local- to global-level molecular epidemiological characterisation of global antimicrobial resistance surveillance system pathogens

The prime goal of molecular epidemiology is to identify the origin and evolution of pathogens, which can potentially influence the public health worldwide. Traditional methods provide limited information which is not sufficient for outbreak investigation and studying transmission dynamics. The recent advancement of next-generation sequencing had a major impact on molecular epidemiological studies. Currently, whole-genome sequencing (WGS) has become the gold standard typing method, especially for clinically significant pathogens. Here, we aimed to describe the application of appropriate molecular typing methods for global antimicrobial resistance surveillance system pathogens based on the level of discrimination and epidemiological settings. This shows that sequence-based methods such as multi-locus sequence typing (MLST) are widely used due to cost-effectiveness and database accessibility. However, WGS is the only method of choice for studying Escherichia coli and Shigella spp. WGS is shown to have higher discrimination than other methods in typing Klebsiella pneumoniae, Acinetobacter baumannii and Salmonella spp. due to its changing accessory genome content. For Gram positives such as Streptococcus pneumoniae, WGS would be preferable to understand the evolution of the strains. Similarly, for Staphylococcus aureus, combination of MLST, staphylococcal protein A or SCCmec typing along with WGS could be the choice for epidemiological typing of hospital- and community-acquired strains. This review highlights that combinations of different typing methods should be used to get complete information since no one standalone method is sufficient to study the varying genome diversity.