Antibiotic Resistance-associated Genes Research Articles

A comprehensive review on epigenetic and epitranscriptomic-mediated regulation of antibiotic resistance

Antibiotic resistance is the leading cause of death globally, with a higher possibility of the emergence of highly resistant pathogens, leading to epidemics. Several antibiotic resistance mechanisms have been discovered, such as enhanced efflux of antibiotics, reduced influx of antibiotics, alteration of antibiotics or their targets, and adaptation to antibiotics. However, this mechanism cannot fully explain the development of antibiotic resistance because the genes associated with this mechanism have been elucidated. However, the factors governing their regulation are not yet fully understood. Recent studies have highlighted the epigenetic and epitranscriptomic roles of antibiotic resistance development-associated genes. Epigenetic modification is associated with DNA modification, whereas epitranscriptomic modification is associated with RNA modification to control gene expression by regulating various biological phenomena such as splicing, translation, and stability. Therefore, this review will focus on the discovery of epigenetic modifications, particularly by DNA methyltransferases, such as restriction-modification (R-M) systems associated with methyltransferases, orphan DNA methyltransferases, and nucleoid-associated proteins that contribute to the development of antibiotic resistance. This scrutinization further expands to epitranscriptomic modification of non-coding RNA, which has a role in the regulation of antibiotic resistance. Epitranscriptomic modification of ribosomal RNA (rRNA), which is a major target of antibiotics, has been well explored. while non-coding RNA such as cis and trans small non coding RNA, and riboswitches are poorly explored. This epigenetic and epitranscriptomic modification will help to understand the regulation of antibiotic resistance-associated genes, which will help to identify key regulators of antibiotic resistance, paving the way for new antibiotic discovery, leading to decreased antibiotic mortality globally.

Extensively drug-resistant Enterobacter ludwigii co-harbouring MCR-9 and a multicopy of blaIMP-1 in South Korea

In this study, we describe an Enterobacter ludwigii clinical isolate that is resistant to both carbapenems and colistin in South Korea. Antimicrobial susceptibility testing revealed that E. ludwigii CRE2104-31 was non-susceptible to all tested antibiotics except fosfomycin. Whole genome sequencing identified a 323-kbp IncHI2 plasmid, pCRE2104-31a, that was co-harbouring mobile colistin resistance (mcr)-9.1 and blaIMP-1. In comparison with other full plasmids, pCRE2104-31a exhibited the closest similarity to a plasmid from the Klebsiella pneumoniae strain CNR48 from France, with 19.9% query coverage and 99% identity. Notably, we observed five tandem repeats of blaIMP-1 and aac(6′)-Il genes, accompanied by multiple attCs within a class I integron on the Tn402-like transposon. The unit of blaIMP-1-attC-aac(6′)-Il-attC might have accumulated due to multiple convergent events. In addition to mcr-9.1 and blaIMP-1, various other antibiotic resistance-associated genes were identified in the plasmid, as follows: blaTEM-1B, aph(3′)-I, aph(3′)-Ia, aac(6′)-Il, aac(6′)-IIc, aac(6′)-IIa, aph(6)-Id, aph(3′')-Ib, aadA2b, aac(6′)-Ib3, sul, dfrA19, qnrB2, aac(6′)-Ib-cr, ere(A), and qacE. A conjugation assay showed that the mcr-9.1/blaIMP-1-co-bearing plasmid was self-transmissible to E. coli J53. However, colistin and carbapenem resistance could not be transferred to E. coli due to high incompatibility. The convergence of mcr and carbapenemase genes is thought to be host-dependent among Enterobacteriaceae. The emergence of extensively drug-resistant E. ludwigii co-harbouring MCR-9.1 and a multicopy of blaIMP-1 would pose a significant threat within the compatible Enterobacteriaceae.

Identifying sources of antibiotic resistance genes in the environment using the microbial Find, Inform, and Test framework.

Antimicrobial resistance (AMR) is an increasing public health concern for humans, animals, and the environment. However, the contributions of spatially distributed sources of AMR in the environment are not well defined. To identify the sources of environmental AMR, the novel microbial Find, Inform, and Test (FIT) model was applied to a panel of five antibiotic resistance-associated genes (ARGs), namely, erm(B), tet(W), qnrA, sul1, and intI1, quantified from riverbed sediment and surface water from a mixed-use region. A one standard deviation increase in the modeled contributions of elevated AMR from bovine sources or land-applied waste sources [land application of biosolids, sludge, and industrial wastewater (i.e., food processing) and domestic (i.e., municipal and septage)] was associated with 34-80% and 33-77% increases in the relative abundances of the ARGs in riverbed sediment and surface water, respectively. Sources influenced environmental AMR at overland distances of up to 13 km. Our study corroborates previous evidence of offsite migration of microbial pollution from bovine sources and newly suggests offsite migration from land-applied waste. With FIT, we estimated the distance-based influence range overland and downstream around sources to model the impact these sources may have on AMR at unsampled sites. This modeling supports targeted monitoring of AMR from sources for future exposure and risk mitigation efforts.

Genetic diversity, antibiotic resistance, and virulence characteristics of Staphylococcus aureus from raw milk over 10 years in Shanghai

Staphylococcus aureus (S. aureus) is a major cause of foodborne infections and its persistence in raw milk is a multifaceted phenomenon that poses a considerable public health challenge. Our study investigated the prevalence, virulence genes, antibiotic resistance, and genetic characterization of S. aureus in raw milk in six Shanghai districts from 2013 to 2022. At 18 dairy farms, a total of 704 S. aureus strains were isolated from 1799 samples tested for drug sensitivity. The highest rates of antibiotic resistance were ampicillin (96.7 %), sulfamethoxazole (65 %), and erythromycin (21.6 %). Between 2018 and 2022, there was a significant decrease in the resistance rates of ceftiofur, ofloxacin, tilmicosin, erythromycin, clindamycin, amoxicillin-clavulanic acid, and sulfamethoxazole in comparison to the period from 2013 to 2017. There were 205 S. aureus strains chosen for whole genome sequencing (WGS), with no more than 2 strains of the same resistance phenotype from each farm per year. The prevalence of mecA-positive strains was 14.15 %, while other antibiotic resistance-associated genes were observed as follows: blaI (70.21 %), lnu(B) (5.85 %), lsa(E) (5.75 %), fexA (6.83 %), erm(C) (4.39 %), tet(L) (9.27 %), and dfrG (5.85 %). Isolates harboring the immune evasion cluster (IEC) genes (scn, chp, and sak) were predominantly categorized as sequence types (STs) 7, 188, 15, 59, and 398. The predominant cluster complexes were CC97, CC1, CC398, and CC1651. In 2017–2022, there was a transition in CC1 from the highly antibiotic-resistant ST9 strain that emerged between 2013 and 2018 to the low-resistant but highly virulent ST1 strain. Retrospective phylogenetic analysis elucidated the evolutionary history of the isolates and demonstrated that the human-animal host transition of S. aureus was linked to the genesis of MRSA CC398. The implementation of extended surveillance will aid in the development of innovative strategies to avoid the transmission of S. aureus along the dairy food chain and the occurrence of public health events.

Molecular typing and drug resistance analysis of carbapenem-resistant Klebsiella pneumoniae from paediatric patients in China.

There are few studies on paediatric carbapenem-resistant Klebsiella pneumoniae (CRKP) in China. The present study investigated the molecular epidemiological and drug resistance characteristics of CRKP from paediatric patients in China to provide a reference for the prevention and control of CRKP infection. In total, 20 nonrepetitive clinical CRKP isolates were collected between February 2019 and February 2020 in a tertiary hospital in China. Strain identification and drug susceptibility testing were carried out using the VITEK® 2 Compact Bacterial Identification and Monitoring System. Sequence typing, phylogenetic relationships, and antibiotic resistance-associated genes were analysed by whole genome sequencing (WGS). sequence typing (MLST) and Core genome multilocus sequence typing (cgMLST) analysis revealed the most frequently represented were ST2407-CT3536 (30%), ST76-CT5893 (25%), and ST309-CT7864 (25%). All 20 CRKP isolates were divided into three clusters. All isolates were highly resistant to a variety of β-lactams and were highly susceptible to quinolones, aminoglycosides, and sulphonamides. All isolates mainly carried the carbapenem resistance genes blaNDM-1 and blaKPC-2, among which 10 isolates carried both blaNDM-1 and blaKPC-2 simultaneously. Sequence typing, phylogenetic relationships, and antibiotic resistance genes can be determined using WGS technology. This can guide CRKP infection control and clinical treatment for paediatric patients.

Equine sinusitis aetiology is linked to sinus microbiome by amplicon sequencing.

Information regarding the microbiome in sinusitis using genetic sequencing is lacking and more-in-depth understanding of the microbiome could improve antimicrobial selection and treatment outcomes for cases of primary sinusitis. To describe sinus microbiota in samples from horses with sinusitis and compare microbiota and the presence of antimicrobial resistance genes between primary, dental-related and other secondary causes of sinusitis. Retrospective case series. Records of equine sinusitis from 2017 to 2021 were reviewed and historical microbial amplicon sequence data were obtained from clinical diagnostic testing of sinus secretions. Following bioinformatic processing of bacterial and fungal sequence data, the sinus microbiota and importance of sinusitis aetiology among other factors were investigated from the perspectives of alpha diversity (e.g., number of operational taxonomic units [OTUs], Hill1 Diversity), beta diversity, and differentially abundant taxa. Quantitative PCR allowed for comparisons of estimated bacterial abundance and detection rate of common antibiotic resistance-associated genes. In a smaller subset, longitudinal analysis was performed to evaluate similarity in samples over time. Of 81 samples analysed from 70 horses, the bacterial microbiome was characterised in 66, and fungal in five. Only sinusitis aetiology was shown to significantly influence microbiome diversity and composition (p< 0.05). Dental-related sinusitis (n= 44) was associated with a significantly higher proportion of obligate anaerobic bacteria, whereas primary sinusitis (n= 12) and other (n= 10) groups were associated with fewer bacteria and higher proportions of facultative anaerobic and aerobic genera. Antimicrobial resistance genes and fungal components were exclusively identified in dental-related sinusitis. Retrospective nature, incomplete prior antimicrobial administration data. Molecular characterisation in sinusitis identifies microbial species which may be difficult to isolate via culture, and microbiome profiling can differentiate sinusitis aetiology, which may inform further treatment, including antimicrobial therapy.

Assessment of Antibiotic Resistance and Efflux Pump Gene Expression in Neisseria Gonorrhoeae Isolates from South Africa by Quantitative Real-Time PCR and Regression Analysis.

Introduction Treatment of gonorrhoea infection is limited by the increasing prevalence of multidrug-resistant strains. Cost-effective molecular diagnostic tests can guide effective antimicrobial stewardship. The aim of this study was to correlate mRNA expression levels in Neisseria gonorrhoeae antibiotic target genes and efflux pump genes to antibiotic resistance in our population. Methods This study investigated the expression profile of antibiotic resistance-associated genes (penA, ponA, pilQ, mtrR, mtrA, mtrF, gyrA, parC, parE, rpsJ, 16S rRNA, and 23S rRNA) and efflux pump genes (macAB, norM, and mtrCDE), by quantitative real-time PCR, in clinical isolates from KwaZulu-Natal, South Africa. Whole-genome sequencing was used to determine the presence or absence of mutations. Results N. gonorrhoeae isolates, from female and male patients presenting for care at clinics in KwaZulu-Natal, South Africa, were analysed. As determined by binomial regression and ROC analysis, the most significant (p ≤ 0.05) markers for resistance prediction in this population, and their cutoff values, were determined to be mtrC (p = 0.024; cutoff <0.089), gyrA (p = 0.027; cutoff <0.0518), parE (p = 0.036; cutoff <0.0033), rpsJ (p = 0.047; cutoff <0.0012), and 23S rRNA (p = 0.042; cutoff >7.754). Conclusion Antimicrobial stewardship includes exploring options to conserve currently available drugs for gonorrhoea treatment. There is the potential to predict an isolate as either susceptible or nonsusceptible based on the mRNA expression level of specific candidate markers, to inform patient management. This real-time qPCR approach, with few targets, can be further investigated for use as a potentially cost-effective diagnostic tool to detect resistance.

Genomic analysis of the nomenclatural type strain of the nematode-associated entomopathogenic bacterium Providencia vermicola

BackgroundEnterobacteria of the genus Providencia are mainly known as opportunistic human pathogens but have been isolated from highly diverse natural environments. The species Providencia vermicola comprises insect pathogenic bacteria carried by entomoparasitic nematodes and is investigated as a possible insect biocontrol agent. The recent publication of several genome sequences from bacteria assigned to this species has given rise to inconsistent preliminary results.ResultsThe genome of the nematode-derived P. vermicola type strain DSM_17385 has been assembled into a 4.2 Mb sequence comprising 5 scaffolds and 13 contigs. A total of 3969 protein-encoding genes were identified. Multilocus sequence typing with different marker sets revealed that none of the previously published presumed P. vermicola genomes represents this taxonomic species. Comparative genomic analysis has confirmed a close phylogenetic relationship of P. vermicola to the P. rettgeri species complex. P. vermicola DSM_17385 carries a type III secretion system (T3SS-1) with probable function in host cell invasion or intracellular survival. Potentially antibiotic resistance-associated genes comprising numerous efflux pumps and point-mutated house-keeping genes, have been identified across the P. vermicola genome. A single small (3.7 kb) plasmid identified, pPVER1, structurally belongs to the qnrD-type family of fluoroquinolone resistance conferring plasmids that is prominent in Providencia and Proteus bacteria, but lacks the qnrD resistance gene.ConclusionsThe sequence reported represents the first well-supported published genome for the taxonomic species P. vermicola to be used as reference in further comparative genomics studies on Providencia bacteria. Due to a striking difference in the type of injectisome encoded by the respective genomes, P. vermicola might operate a fundamentally different mechanism of entomopathogenicity when compared to insect-pathogenic Providencia sneebia or Providencia burhodogranariea. The complete absence of antibiotic resistance gene carrying plasmids or mobile genetic elements as those causing multi drug resistance phenomena in clinical Providencia strains, is consistent with the invertebrate pathogen P. vermicola being in its natural environment efficiently excluded from the propagation routes of multidrug resistance (MDR) carrying genetic elements operating between human pathogens. Susceptibility to MDR plasmid acquisition will likely become a major criterion in the evaluation of P. vermicola for potential applications in biological pest control.

Comparative Whole Genome Sequence Analysis and Biological Features of Clostridioides difficile Sequence Type 2‡.

Clostridioides difficile sequence type 2 (ST2) has been increasingly recognized as one of the major genotypes in China, while the genomic characteristics and biological phenotypes of Chinese ST2 strains remain to be determined. We used whole-genome sequencing and phylogenetic analysis to investigate the genomic features of 182 ST2 strains, isolated between 2011 and 2017. PCR ribotyping (RT) was performed, and antibiotic resistance, toxin concentration, and sporulation capacity were measured. The core genome Maximum-likelihood phylogenetic analysis showed that ST2 strains were distinctly segregated into two genetically diverse lineages [L1 (67.0% from Northern America) and L2], while L2 further divided into two sub-lineages, SL2a and SL2b (73.5% from China). The 36 virulence-related genes were widely distributed in ST2 genomes, but in which only 11 antibiotic resistance-associated genes were dispersedly found. Among the 25 SL2b sequenced isolates, RT014 (40.0%, n = 10) and RT020 (28.0%, n = 7) were two main genotypes with no significant difference on antibiotic resistance (χ2 = 0.024–2.667, P > 0.05). A non-synonymous amino acid substitution was found in tcdB (Y1975D) which was specific to SL2b. Although there was no significant difference in sporulation capacity between the two lineages, the average toxin B concentration (5.11 ± 3.20 ng/μL) in SL2b was significantly lower in comparison to those in L1 (10.49 ± 15.82 ng/μL) and SL2a (13.92 ± 2.39 ng/μL) (χ2 = 12.30, P < 0.05). This study described the genomic characteristics of C. difficile ST2, with many virulence loci and few antibiotic resistance elements. The Chinese ST2 strains with the mutation in codon 1975 of the tcdB gene clustering in SL2b circulating in China express low toxin B, which may be associated with mild or moderate C. difficile infection.

High prevalence of circulating dual-class resistant Mycoplasma genitalium in asymptomatic MSM in Tokyo, Japan.

ObjectivesTo assess the prevalence and antibiotic resistance profile of Mycoplasma genitalium detected from urogenital/rectal swab samples obtained from MSM in Tokyo, Japan.MethodsWe performed PCR-based screening for M. genitalium urogenital/rectal infection in 982 asymptomatic MSM between 1 January 2019 and 5 November 2020. Mutations in the antibiotic resistance-associated genes gyrA and parC and the 23S rRNA of M. genitalium were analysed.ResultsThe prevalence of M. genitalium infection was 6.1%: the prevalence of rectal and urogenital infection was 4.7% and 1.4%, respectively. Among the cases, 48 were successfully analysed for 23S rRNA, 41 for parC mutations and 37 for gyrA mutations. Macrolide- and quinolone-resistance associated mutations (23S rRNA and parC mutations) were observed in 43 (89.6%) and 28 (68.3%) cases, respectively. The quinolone-resistance associated mutation-harbouring variants also harboured macrolide-resistance associated mutations. The S83I mutation in the parC gene was most commonly identified (24 cases, 58.5%), and its combination with M95I or D99N mutation in the gyrA gene was observed in 9 of 36 successfully analysed cases (25.0%). No significant association was observed between the presence of antibiotic resistance and antibiotic exposure for either macrolides or fluoroquinolones (P = 0.785 and 0.402, respectively).ConclusionsIn Tokyo, there is an alarmingly high prevalence of M. genitalium harbouring macrolide and/or quinolone resistance-associated mutations in MSM, irrespective of antibiotic exposure. The high prevalence of M. genitalium strains with both parC and gyrA mutations limits the efficacy of sitafloxacin. Therefore, suitable alternatives are required to treat such M. genitalium infections.

MICROARRAY-BASED ANALYSIS OF STAPHYLOCOCCUS AUREUS ISOLATES FROM NON-CLINICAL SOURCE

This study was aimed to genotyped virulence, toxin and resistance genes of 30 S. aureus isolates from pigs using DNA microarray. The 30 isolates analyzed in this study all belonged to clonal complexes (CC) CC1 (3; 10%), CC5 (3; 10%), CC15 (16; 53.33%) and CC152 (8; 26.66%), respectively. Of antibiotic resistance-associated genes reported; Twenty out of 30 isolates (66.66%) carried the beta-lactamase operon (blaZ/I/R) and the tetracycline resistance gene (tetK), respectively. Also, the macrolide resistance gene (ermA/msrA) were detected in ten isolates (33.33%), the multidrug efflux pump resistance gene (sdrM) was detected in seven isolates (23.33%) and one isolates (3.33%) harboured the chloramphenicol resistance gene (cat). None of the isolates harboured genes conferring methicillin resistance. In terms of genes encoding enterotoxins; seb was detected among all isolates of CC15 while the enterotoxin gene cluster egc and a distinct variant of the enterotoxin A (sea-N315) were detected among isolates of CC5 and CC152, respectively. Two CC152 isolate was positive for genes encoding the Panton-Valentine leukocidin (lukF-PV+lukS-PV). In addition, all the isolates harboured the genes encoding for intracellular adhesion proteins (icaA/C/D) and the biofilm-associated genes (clfA and clfB) except for CC1 isolates. The capsular genes cap5 and cap8 were detected in isolates of CC5 and CC15 while only cap5 was present in CC152 isolates. The study provides detailed genotyping data on the population structure, presence of toxins and antibiotic resistance markers of S. aureus isolates and indicates the importance of the microarray technique in analyzing multiple gene contents of bacteria.

The impact of DNA adenine methyltransferase knockout on the development of triclosan resistance and antibiotic cross-resistance in Escherichia coli.

Background DNA adenine methyltransferase (dam) has been well documented for its role in regulation of replication, mismatch repair and transposition. Recent studies have also suggested a role for dam in protection against antibiotic stress, although this is not yet fully defined. We therefore evaluated the role of dam in the development of antibiotic resistance and triclosan-associated cross-resistance.Results A significant impact on growth rate was seen in the dam knockout compared to the parental strain. Known triclosan resistance-associated mutations in fabI were seen regardless of dam status, with an additional mutation in lrhA seen in the dam knockout. The expression of multiple antibiotic resistance-associated genes was significantly different between the parent and dam knockout post-resistance induction. Reversion rate assays showed that resistance mechanisms were stable.Conclusions dam knockout had a significant effect on growth, but its role in the development of antibiotic resistance is likely confined to those antibiotics using acrAD-containing efflux pumps.

A broad-spectrum phage controls multidrug-resistant Salmonella in liquid eggs

Salmonella is a foodborne pathogen constantly threating public health. The widespread use of antibiotics and globalization of the food industry result in rapid growth of drug-resistance. Eggs contaminated by multidrug-resistant (MDR) Salmonella are one of the riskiest factors of salmonellosis, which are frequently associated with outbreaks worldwide. Thus, there are increasing needs for the development of new technologies in controlling MDR pathogens and for the confirmation of their practical efficiency in target food matrices. In this study, 43 Salmonella phages were isolated from environmental resources and among them, phage D1-2 was selected since it exhibited the most potent lytic ability and the broadest host spectrum against tested Salmonella strains. Further study demonstrated that D1-2 shows high pH and thermal tolerances and a short latent period, together with a low frequency of emergence of phage resistance. D1-2 effectively inhibited the growth of two MDR Salmonella strains in liquid egg white and egg yolk at both 4 °C and 25 °C. Morphology and phylogeny indicated that D1-2 belongs to the Myoviridae family. Genome analysis of D1-2 revealed a linear dsDNA sequence with no homology to virulence or antibiotic-resistance associated genes, presenting D1-2 is a promising candidate for the biocontrol of MDR Salmonella in highly risky foods.

Investigation of a Pandoraea apista cluster common to adult and paediatric cystic fibrosis patients attending two hospitals in the same city.

We examined evidence for transmission of Pandorea apista among cystic fibrosis (CF) patients attending paediatric and adult services in one city who had previously been found to harbour related isolates by pulsed-field gel electrophoresis (PFGE). The whole-genome sequences of 18 isolates from this cluster from 15 CF patients were examined, along with 2 cluster isolates from 2 other centres. The annotated sequence of one of these, Pa14367, was examined for virulence factors and antibiotic resistance-associated genes in comparison with data from a 'non-cluster' isolate, Pa16226. Single-nucleotide polymorphism (SNP) analysis suggested that cluster isolates from the same city differed from one another by a minimum of 1 and a maximum of 383 SNPs (an average of 213 SNPs; standard deviation: 18.5), while isolates from the 2 other hospitals differed from these by a minimum of 34 and 61 SNPs, respectively. Pa16226 differed from all cluster isolates by a minimum of 22 706 SNPs. Evidence for patient-to-patient transmission among isolates from the same city was relatively limited, although transmission from a common source could not be excluded. The annotated genomes of Pa14367 and Pa16226 carried putative integrative and conjugative elements (ICEs), coding for type IV secretion systems, and genes associated with heavy metal degradation and carbon dioxide fixation, and a wide selection of genes coding for efflux pumps, beta-lactamases and penicillin-binding proteins. Epidemiological analysis suggested that this cluster could not always be attributed to patient-to-patient transmission. The acquisition of ICE-related virulence factors may have had an impact on its prevalence.

Studies of common antibiotic resistance-associated genes of Acinetobacter baumannii

This study, the presence of 4 common beta-lactamase encoding genes including OXA-23, OXA-51, VIM and IMP was determined simultaneously by multiplex PCR, either directly with sputum samples or with purified DNA, giving results within 3-4 hours instead of 2 days compared to the culture method. Within 58 samples positive with Acinetobacter baumannii collected from the hospital, OXA-51 fragment was dominant (81%), whereas, VIM fragment was only identified in one sample (DNA and sputum samples) (1.7%). The antibiograms indicated for 19 samples were used to find correlation between genotype and resistance phenotype.

The clinical significance of carbapenem-resistant Klebsiella pneumoniae rectal colonization in critically ill patients: from colonization to bloodstream infection

To highlight the clinical significance of carbapenem-resistant Klebsiella pneumoniae (CRKP) rectal colonization by examining the risk factors for CRKP rectal colonization and subsequent bloodstream infection (BSI) in critically ill patients. Prospective study of CRKP rectal colonization in an intensive care unit (ICU) during a 39-month period. CRKP strains isolated from both the blood cultures and corresponding rectal specimens (n=96) of patients were screened by PCR for the presence of antibiotic resistance-associated genes. Molecular analyses were conducted to investigate the clonal relatedness of CRKP strains from the rectal and blood specimens. Among the 498 patients, 226 were rectally colonized by CRKP, 48 of whom developed a CRKP BSI. The median time from hospital admission to the detection of CRKP rectal colonization was 8 days, while the median time from colonization to BSI was 4 days. The duration of ICU stay, patient/nurse ratio and prior use of antianaerobic antimicrobials were associated with CRKP rectal colonization. No specific factor was associated with BSIs in the colonized patients. The blaKPC-2 gene was detected in all 96 strains, which were all classified as sequence type ST-258. Representative pairs (n=48) of CRKP strains colonizing and infecting the same patient shared the same pulsotype. Our results indicate that hospitalized patients become infected with their colonizing strains, supporting the strong association between colonization and BSI. Limiting antianaerobic antimicrobial administration, reducing the duration of ICU stay and maintaining a low patient/nurse ratio are possible strategies to restrict rectal CRKP colonization in ICUs.

Investigations by the Institut Hospitalo-Universitaire Méditerranée Infection of food and food-borne infections in the Mediterranean Basin and in sub-Saharan Africa.

Food-borne infections are major causes of public health concern in developing and developed countries. During the past decade, the Institut Hospitalo-Universitaire Méditerranée Infection has conducted or been involved in multiple investigations that aimed at identifying the sources and strains responsible for food-borne diseases and therefore at improving the understanding, diagnosis, prevention and control of these infections. Investigations were conducted in the Mediterranean area and in sub-Saharan Africa on more than 15 food-borne agents, 17 food products and 14 antibiotic resistance-associated genes. Multiple sources, including unexpected ones, and pathogens, including emerging ones, were involved. Travelling in developing countries and zoonoses are major contributors to food-borne infections, while food-borne transmission of resistance-associated genes is increasingly reported. However, risk factors and pathogens associated with food-borne infections likely remain untapped and must be more extensively investigated, monitored and regularly reassessed. Diagnostic tests based on new technologies and real-time surveillance tools based on microbiology laboratory data are promising approaches to detect known food-borne infections and decipher new ones. Studies of the microbiota and its relationships with dietary patterns are also worth being conducted.

Biodegradable Mg-Cu alloy implants with antibacterial activity for the treatment of osteomyelitis: Invitro and invivo evaluations.

Treatment of chronic osteomyelitis (bone infection) remains a clinical challenge; in particular, it requires an implantable material with improved antibacterial activity. Here, we prepared biodegradable magnesium (Mg)-copper (Cu) alloys with different Cu contents (0.05, 0.1, and 0.25wt%) and assessed their potential for treating methicillin-resistant Staphylococcus aureus-induced osteomyelitis. We evaluated the microstructures, mechanical properties, corrosion behavior, and ion release of the alloys invitro, and their biocompatibility and antibacterial activity invitro and invivo. The antibacterial activity of the Mg-Cu alloys invitro was demonstrated by microbiological counting assays, bacterial viability assays, biofilm formation observations, and the expression of biofilm, virulence, and antibiotic-resistance associated genes. The antibacterial activity of Mg-Cu alloys invivo was confirmed by imaging examination, microbiological cultures, and histopathology. The biocompatibility of Mg-Cu alloys was confirmed by cell proliferation, vitality, and morphology assays invitro and Cu(2+) or Mg(2+) ion assays, blood biochemical tests, and histological evaluation invivo. The alloy containing 0.25wt% Cu exhibited the highest antibacterial activity among the tested alloys, with favorable biocompatibility. Collectively, our results indicate the potential utility of Mg-Cu alloy implants with 0.25wt% Cu in treating orthopedic infections.

Genome Sequence of Riemerella anatipestifer Strain RCAD0122, a Multidrug-Resistant Isolate from Ducks

Riemerella anatipestifer is an important pathogenic bacterium in waterfowl and other avian species. We present here the genome sequence of R. anatipestifer RCAD0122, a multidrug-resistant strain isolated from infected ducks. The isolate contains at least nine types of antibiotic resistance-associated genes.

Safety assessment of Lactobacillus plantarum JDM1 based on the complete genome

We performed a comprehensive safety assessment of a probiotic based on the whole genome sequence and corresponding phenotypes. This was performed on Lactobacillus plantarum JDM1, a widely used commercial probiotic strain in China. The minimal inhibitory concentrations (MICs) of sixteen antibiotics and the biogenic amine production of JDM1 were tested to supplement a traditional oral toxicity test. In total, fifty-one antibiotic resistance-associated genes, one hundred twenty-six virulence-associated genes, and twenty-three adverse metabolism-associated genes were found in JDM1. However, there were no toxin or hemolysin encoding genes, and safety-associated genes were rarely transferable. This approach can be generalized to provide a deep safety investigation of novel probiotic strains and greatly reveal the potential danger determinants and their molecular mechanisms. However, this kind of analysis reveals the theoretical maximum risk level as not all genes are efficient depending on environmental conditions.