Susceptibility of clinical isolates of meticillin-resistant Staphylococcus aureus and phenotypic non-extended-spectrum β-lactamase-producing Klebsiella pneumoniae to ceftaroline in Taiwan: Results from Antimicrobial Testing Leadership and Surveillance (ATLAS) in 2012-2018 and Surveillance of Multicentre Antimicrobial Resistance in Taiwan (SMART) in 2018-2019

Evaluating NG-Test CARBA 5 Multiplex Immunochromatographic and Cepheid Xpert CARBA-R Assays among Carbapenem-Resistant Enterobacterales Isolates Associated with Bloodstream Infection

Decreased susceptibility to carbapenems in Enterobacterales is an emerging concern. Conventional methods with short turnaround times are crucial for therapeutic decisions and infection control. In the current study, we used the Xpert CARBA-R (Cepheid, Sunnyvale, CA, USA) and the NG-Test CARBA 5 (NG Biotech, Guipry, France) assays for carbapenemase detection in 214 carbapenem-resistant Enterobacterales (CRE) blood isolates. We used the modified carbapenem inactivation method, conventional PCR, and sequencing to determine the production of five common carbapenemase families and their subtypes. We performed wzc-genotyping for all CR-Klebsiella pneumoniae (CRKP) and multilocus sequence typing for all carbapenemase-producing CRE isolates to reveal their genetic relatedness. The results showed a sensitivity of 99.8% and a specificity of 100% by the Xpert assay, and a sensitivity of 100% and a specificity of 99% by the NG-Test in detecting carbapenemases of 84 CRKP isolates with only one (VIM-1+IMP-8) failure in both tests. For CR-Escherichia coli, four carbapenemase-producing isolates were detected accurately for their subtypes. The two major clones of carbapenemase-producing CRKP isolates in Taiwan were ST11-K47 producing KPC-2 (n = 47) and ST11-K64 producing OXA-48-like (n = 9). Our results support the use of either test in routine laboratories for the rapid detection of common carbapenemases. Caution should be taken using the Xpert assay in areas with a high prevalence of CRE carrying bla_IMP-8. IMPORTANCE Carbapenemase-producing Enterobacterales (CPE) are emerging worldwide, causing nosocomial outbreaks and even community-acquired infections since their appearance 2 decades ago. Our previous national surveillance of CPE isolates in Taiwan identified five carbapenemase families (KPC, OXA, NDM, VIM, and IMP) with the KPC-2 and OXA-48-like types predominant. Timely detection and classification of carbapenemases in CPE may be a useful test to guide optimal therapy and infection control. Genetic detection methods using the Xpert CARBA-R assay and the immunochromatographic assay using the NG-Test CARBA 5 have been validated with the advantage of short turnaround time. Our study demonstrated that the NG and Xpert assays are convenient methods to accurately identify carbapenemases in carbapenem-resistant Klebsiella pneumoniae and carbapenem-resistant Escherichia coli blood isolates. Detecting IMP variants remains challenging, and the results of Xpert CARBA-R assay should be carefully interpreted.

Comparison of Etest and broth microdilution for evaluating the susceptibility of Staphylococcus aureus and Streptococcus pneumoniae to ceftaroline and of carbapenem-resistant Enterobacterales and Pseudomonas aeruginosa to ceftazidime/avibactam

OBJECTIVES

Decreased susceptibility to ceftazidime/avibactam (CZA) and ceftaroline (CPT) has been reported during antimicrobial resistance surveillance and therapy. Conventional laboratories are unable to provide timely susceptibility testing for CZA and CPT because these antimicrobial agents are not incorporated in automated susceptibility testing systems.

METHODS

We evaluated Etest and the Sensititre broth microdilution (BMD) method for testing CZA against carbapenem-resistant Gram-negative bacilli and CPT against important Gram-positive cocci bloodstream isolates. Genotypes of carbapenemases in Enterobacterales were also determined using the Xpert® Carba-R assay.

RESULTS

Etest showed ≥90% agreement with Sensititre BMD for carbapenem-resistant Klebsiella pneumoniae (CRKP) (n = 187), carbapenem-resistant Escherichia coli (CREC) (n = 28) and Streptococcus pneumoniae (n = 35); however, the very major error rate exceeded 3%. Agreement between Etest and Sensititre BMD was <90% for carbapenem-resistant Pseudomonas aeruginosa (CRPA) (n = 81), methicillin-susceptible Staphylococcus aureus (MSSA) (n = 92) and methicillin-resistant S. aureus (MRSA) (n = 170). Both agents remained potent with a high susceptibility rate by Sensititre BMD as follows: CZA against CRKP (95.0%), CREC (89.3%) and CRPA (84.5%); and CPT against MSSA (100.0%), MRSA (95.3%) and S. pneumoniae (94.3%). CZA was active against blaKPC-carrying CRKP (98.5% susceptible), and resistance in the majority of CZA-resistant Enterobacterales isolates (6 of 10 CRKP and 2 of 3 CREC) was due to the presence of a metallo-β-lactamase gene.

CONCLUSION

Our results suggest that interpretation of susceptibility results obtained by Etest for both agents should be undertaken cautiously and remains challenging.

Putative mobilized colistin resistance genes in the human gut microbiome

BACKGROUND

The high incidence of bacterial genes that confer resistance to last-resort antibiotics, such as colistin, caused by mobilized colistin resistance (mcr) genes, poses an unprecedented threat to human health. Understanding the spread, evolution, and distribution of such genes among human populations will help in the development of strategies to diminish their occurrence. To tackle this problem, we investigated the distribution and prevalence of potential mcr genes in the human gut microbiome using a set of bioinformatics tools to screen the Unified Human Gastrointestinal Genome (UHGG) collection for the presence, synteny and phylogeny of putative mcr genes, and co-located antibiotic resistance genes.

RESULTS

A total of 2079 antibiotic resistance genes (ARGs) were classified as mcr genes in 2046 metagenome assembled genomes (MAGs), distributed across 1596 individuals from 41 countries, of which 215 were identified in plasmidial contigs. The genera that presented the largest number of mcr-like genes were Suterella and Parasuterella. Other potential pathogens carrying mcr genes belonged to the genus Vibrio, Escherichia and Campylobacter. Finally, we identified a total of 22,746 ARGs belonging to 21 different classes in the same 2046 MAGs, suggesting multi-resistance potential in the corresponding bacterial strains, increasing the concern of ARGs impact in the clinical settings.

CONCLUSION

This study uncovers the diversity of mcr-like genes in the human gut microbiome. We demonstrated the cosmopolitan distribution of these genes in individuals worldwide and the co-presence of other antibiotic resistance genes, including Extended-spectrum Beta-Lactamases (ESBL). Also, we described mcr-like genes fused to a PAP2-like domain in S. wadsworthensis. These novel sequences increase our knowledge about the diversity and evolution of mcr-like genes. Future research should focus on activity, genetic mobility and a potential colistin resistance in the corresponding strains to experimentally validate those findings.

Molecular and Anti-Microbial Resistance (AMR) Profiling of Methicillin-Resistant Staphylococcus aureus (MRSA) from Hospital and Long-Term Care Facilities (LTCF) Environment

To provide evidence of the cross-contamination of emerging pathogenic microbes in a local network between long-term care facilities (LTCFs) and hospitals, this study emphasizes the molecular typing, the prevalence of virulence genes, and the antibiotic resistance pattern of methicillin-resistant Staphylococcus aureus. MRSA isolates were characterized from 246 samples collected from LTCFs, medical tubes of LTCF residents, and hospital environments of two cities, Chiayi and Changhua. Species identification, molecular characterization, and drug resistance analysis were performed. Hospital environments had a higher MRSA detection rate than that of LTCF environments, where moist samples are a hotspot of MRSA habitats, including tube samples from LTCF residents. All MRSA isolates in this study carried the exfoliative toxin eta gene (100%). The majority of MRSA isolates were resistant to erythromycin (76.7%), gentamicin (60%), and ciprofloxacin (55%). The percentage of multidrug-resistant MRSA isolates was approximately 50%. The enterobacterial repetitive intergenic consensus polymerase chain reaction results showed that 18 MRSA isolates belonged to a specific cluster. This implied that genetically similar isolates were spread between hospitals and LTCFs in Changhua city. This study highlights the threat to the health of LTCFs’ residents posed by hospital contact with MRSA.

High-level ceftaroline resistance in a paediatric patient with invasive methicillin-resistant Staphylococcus aureus infection without previous ceftaroline exposure

WHAT IS KNOWN AN OBJECTIVE

Our objective is to report a paediatric case of high-level ceftaroline resistance without previous ceftaroline exposure.

CASE DESCRIPTION

A 20-month-old, 12 kg, female with invasive MRSA infection presented with high-level ceftaroline resistance with no previous ceftaroline exposure.

WHAT IS NEW AND CONCLUSION

To our knowledge, our case is the first report of high-level ceftaroline resistance evident in a paediatric patient with invasive infection due to MRSA, without history of prior ceftaroline exposure. This case illustrates the importance of weighing the risk of resistance with the benefits of use when starting therapy empirically prior to susceptibility results, even in patients without previous drug exposure.