Acquisition of high-level mupirocin resistance and its fitness cost among methicillin-resistant Staphylococcus aureus strains with low-level mupirocin resistance

Prevalence of carbapenemase-producing organisms at the Kidney Center of Rawalpindi (Pakistan) and evaluation of an advanced molecular microarray-based carbapenemase assay

AIM

A DNA microarray-based assay for the detection of antimicrobial resistance (AMR) genes was used to study carbapenemase-producing organisms at the Kidney Center of Rawalpindi, Pakistan.

METHODS

The evaluation of this assay was performed using 97 reference strains with confirmed AMR genes. Testing of 7857 clinical samples identified 425 Gram-negative bacteria out of which 82 appeared carbapenem resistant. These isolates were analyzed using VITEK-2 for phenotyping and the described AMR assay for genotyping.

RESULTS

The most prevalent carbapenemase gene was blaNDM and in 12 isolates we detected two carbapenemase genes (e.g., blaNDM/blaOXA-48).

CONCLUSION

Our prevalence data from Pakistan show that - as in other parts of the world - carbapenemase-producing organisms with different underlying resistance mechanisms are emerging, and this warrants intensified and constant surveillance.

Testing the role of genetic background in parallel evolution using the comparative experimental evolution of antibiotic resistance

Parallel evolution is the independent evolution of the same phenotype or genotype in response to the same selection pressure. There are examples of parallel molecular evolution across divergent genetic backgrounds, suggesting that genetic background may not play an important role in determining the outcome of adaptation. Here, we measure the influence of genetic background on phenotypic and molecular adaptation by combining experimental evolution with comparative analysis. We selected for resistance to the antibiotic rifampicin in eight strains of bacteria from the genus Pseudomonas using a short term selection experiment. Adaptation occurred by 47 mutations at conserved sites in rpoB, the target of rifampicin, and due to the high diversity of possible mutations the probability of within-strain parallel evolution was low. The probability of between-strain parallel evolution was only marginally lower, because different strains substituted similar rpoB mutations. In contrast, we found that more than 30% of the phenotypic variation in the growth rate of evolved clones was attributable to among-strain differences. Parallel molecular evolution across strains resulted in divergent phenotypic evolution because rpoB mutations had different effects on growth rate in different strains. This study shows that genetic divergence between strains constrains parallel phenotypic evolution, but had little detectable impact on the molecular basis of adaptation in this system.

Mupirocin-induced mutations in ileS in various genetic backgrounds of methicillin-resistant Staphylococcus aureus

Topical mupirocin is widely used for the decolonization of methicillin-resistant Staphylococcus aureus (MRSA) carriers. We evaluated the capacity of various MRSA clonotypes to develop mutations in the ileS gene associated with low-level mupirocin resistance. Twenty-four mupirocin-sensitive MRSA isolates from a variety of genotypes (determined by a multilocus variable-number tandem-repeat assay) were selected. Mupirocin MICs were determined by Etest. The isolates were then incubated in subinhibitory concentrations of mupirocin for 7 to 14 days. Repeat MIC determinations and sequencing of the ileS gene were then performed. Doubling times of isolates exposed to mupirocin and of unexposed isolates were compared. We found that exposure to mupirocin led to rapid induction of low-level resistance (MICs of 8 to 24 μg/ml) in 11 of 24 (46%) MRSA isolates. This phenomenon was observed in strains with diverse genetic backgrounds. Various mutations were detected in 18 of 24 (75%) MRSA isolates. Acquisition of mutations appeared to be a stepwise process during prolonged incubation with the drug. Among the five isolates exhibiting low-level resistance and the highest MICs, four tested sensitive after incubation in the absence of mupirocin but there was no reversion to the susceptible wild-type primary sequence. Resistance was not associated with significant fitness cost, suggesting that MRSA strains with low-level mupirocin resistance may have a selective advantage in facilities where mupirocin is commonly used. Our findings emphasize the importance of the judicious use of this topical agent and the need to closely monitor for the emergence of resistance.

Large mobile genetic elements carrying resistance genes that do not confer a fitness burden in healthcare-associated meticillin-resistant Staphylococcus aureus

Healthcare-associated (HA) meticillin-resistant Staphylococcus aureus (MRSA) clone CC22 SCCmecIV (EMRSA-15) has recently overtaken CC30/ST36 SCCmecII (EMRSA-16) as the dominant clone in UK hospitals. CC22 SCCmecIV shows greater fitness than CC30 SCCmecII, although both are successful global pathogens. The aim of this study was to test whether mobile genetic elements (MGEs), specifically SCCmec and large plasmids encoding resistance genes, are a burden and contribute to this fitness difference. Thirty-nine clinical isolates of MRSA and meticillin-sensitive S. aureus from lineages CC30 and CC22 with a variety of antibiotic resistance genes were grown in the absence of antibiotics. A range of relative fitness measures were used to compare clinical isolates with and without SCCmecII and SCCmecIV. The same fitness measures were used to compare eight isolates with and without naturally occurring large antibiotic resistance plasmids carrying gentamicin resistance (determined by microarray) and an isolate with an introduced plasmid. Growth rate, competitive ability during co-culture and survival after desiccation were then compared. Carriage of SCCmecII contributed to the reduced fitness of CC30 MRSA. However, we found no evidence of a fitness cost due to carriage of SCCmecIV in CC22, or large antibiotic resistance plasmids in CC30 or multiple resistances in both lineages. In conclusion, many large MGEs are not a fitness burden. Surprisingly, lineage background was the most important determinant of fitness. Our results suggest CC22 SCCmecIV will remain a successful healthcare-associated clone, and resistance to meticillin and gentamicin is likely to be maintained even in the absence of antibiotic pressure.

Rare occurrence of mupirocin resistance among clinical Staphylococcus isolates in Jordan

Staphylococcal infections have high occurrence in Jordanian patients. This study was carried out to determine the rates of high- and low-level mupirocin resistance (MupH and MupL) among staphylococci with the molecular characterization. Two hundred and thirty-two non-duplicate Staphylococcus spp. isolated from different clinical specimens were tested for mupirocin susceptibility using disk diffusion method and minimum inhibitory concentration (MIC). Resistance genes and clone relatedness was studied using polymerase chain reaction (PCR) and enterobacterial repetitive intergenic consensus primers (Eric-PCR) for the latter. Plasmid curing was performed to determine the genetic location of MupA gene. Among the 232 strains, 144 (62%) were methicillin-resistant Staphylococcus aureus (MRSA), 33 (14.2%) methicillin-susceptible Staphylococcus aureus (MSSA) and 55 (23.7%) were of other coagulase-negative Staphylococcus spp. (CoNS). Of all strains tested, only 6 (2.6%) were mupirocin resistant. MecA gene was detected in both MupL and MupH strains but MupA gene was only detected in MupH. Plasmid curing improved the plasmidic location of MupA gene. Molecular typing by Eric-PCR method revealed heterogenicity of the genetic make up of our MupL and MupH strains. Staphylococci with MupA-carrying genes are present in Jordanian hospitals, but thank to the limited use of mupirocin, they remain rare.