Prevalence and antimicrobial resistance pattern of Clostridium difficile among hospitalized diarrheal patients: A systematic review and meta-analysis

Background Clostridium difficile is the leading cause of infectious diarrhea that develops in patients after hospitalization during antibiotic administration. It has also become a big issue in community-acquired diarrhea. The emergence of hypervirulent strains of C. difficile poses a major problem in hospital-associated diarrhea outbreaks and it is difficult to treat. The antimicrobial resistance in C. difficile has worsened due to the inappropriate use of broad-spectrum antibiotics including cephalosporins, clindamycin, tetracycline, and fluoroquinolones together with the emergence of hypervirulent strains. Objective To estimate the pooled prevalence and antimicrobial resistance pattern of C. difficile derived from hospitalized diarrheal patients, a systematic review and meta-analysis was performed. Methods Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guideline was followed to review published studies conducted. We searched bibliographic databases from PubMed, Scopus, Google Scholar, and Cochrane Library for studies on the prevalence and antimicrobial susceptibility testing on C. difficile. The weighted pooled prevalence and resistance for each antimicrobial agent was calculated using a random-effects model. A funnel plot and Egger’s regression test were used to see publication bias. Results A total of 15 studies were included. Ten articles for prevalence study and 5 additional studies for antimicrobial susceptibility testing of C. difficile were included. A total of 1967/7852 (25%) C. difficile were isolated from 10 included studies for prevalence study. The overall weighted pooled proportion (WPP) of C. difficile was 30% (95% CI: 10.0–49.0; p<0.001). The analysis showed substantial heterogeneity among studies (Cochran’s test = 7038.73, I2 = 99.87%; p<0.001). The weighed pooled antimicrobial resistance (WPR) were: vancomycin 3%(95% CI: 1.0–4.0, p<0.001); metronidazole 5%(95% CI: 3.0–7.0, p<0.001); clindamycin 61%(95% CI: 52.0–69.0, p<0.001); moxifloxacin 42%(95% CI: 29–54, p<0.001); tetracycline 35%(95% CI: 22–49, p<0.001); erythromycin 61%(95% CI: 48–75, p<0.001) and ciprofloxacin 64%(95% CI: 48–80; p< 0.001) using the random effect model. Conclusions A higher weighted pooled prevalence of C. difficile was observed. It needs a great deal of attention to decrease the prevailing prevalence. The resistance of C. difficile to metronidazole and vancomycin was low compared to other drugs used to treat C. difficile infection. Periodic antimicrobial resistance monitoring is vital for appropriate therapy of C. difficile infection.

A clinical prediction tool for extended-spectrum β-lactamase-producing Enterobacteriaceae urinary tract infection

Background Prevalence of extended-spectrum beta-lactamase-producing-Enterobacteriaceae (ESBL-E) has risen in patients with urinary tract infections. The objective of this study was to determine explore the risk factors of ESBL-E infection in hospitalized patients and establish a predictive model. Methods This retrospective study included all patients with an Enterobacteriaceae-positive urine sample at the first affiliated hospital of Jinan university from January 2018 to December 2019. Antimicrobial susceptibility patterns of ESBL-E were analyzed, and multivariate analysis of related factors was performed. From these, a nomogram was established to predict the possibility of ESBL-E infection. Simultaneously, susceptibility testing of a broad array of carbapenem antibiotics was performed on ESBL-E cultures to explore possible alternative treatment options. Results Of the total 874 patients with urinary tract infections (UTIs), 272 (31.1%) were ESBL-E positive. In the predictive analysis, five variables were identified as independent risk factors for ESBL-E infection: male gender (OR = 1.607, 95% CI 1.066–2.416), older age (OR = 4.100, 95% CI 1.678–12.343), a hospital stay in preceding 3 months (OR = 1.872, 95% CI 1.141–3.067), invasive urological procedure (OR = 1.810, 95% CI 1.197–2.729), and antibiotic use within the previous 3 months (OR = 1.833, 95% CI 1.055–3.188). In multivariate analysis, the data set was divided into a training set of 611 patients and a validation set of 263 patients The model developed to predict ESBL-E infection was effective, with the AuROC of 0.650 (95% CI 0.577–0.725). Among the antibiotics tested, several showed very high effectiveness against ESBL-E: amikacin (85.7%), carbapenems (83.8%), tigecycline (97.1%) and polymyxin (98.2%). Conclusions The nomogram is useful for estimating a UTI patient’s likelihood of infection with ESBL-E. It could improve clinical decision making and enable more efficient empirical treatment. Empirical treatment may be informed by the results of the antibiotic susceptibility testing.

Genomic evolution of the globally disseminated multidrug-resistant Klebsiella pneumoniae clonal group 147

The rapid emergence of multidrug-resistant Klebsiella pneumoniae is being driven largely by the spread of specific clonal groups (CGs). Of these, CG147 includes 7-gene multilocus sequence typing (MLST) sequence types (STs) ST147, ST273 and ST392. CG147 has caused nosocomial outbreaks across the world, but its global population dynamics remain unknown. Here, we report a pandrug-resistant ST147 clinical isolate from India (strain DJ) and define the evolution and global emergence of CG147. Antimicrobial-susceptibility testing following European Committee on Antimicrobial Susceptibility Testing (EUCAST) guidelines and genome sequencing (Illumina and Oxford Nanopore Technologies, Unicycler assembly) were performed on strain DJ. Additionally, we collated 217 publicly available CG147 genomes [National Center for Biotechnology Information (NCBI), May 2019]. CG147 evolution was inferred within a temporal phylogenetic framework (beast) based on a recombination-free sequence alignment (Roary/Gubbins). Comparative genomic analyses focused on resistance and virulence genes and other genetic elements (BIGSdb, Kleborate, PlasmidFinder, phaster, ICEfinder and CRISPRCasFinder). Strain DJ had a pandrug-resistance phenotype. Its genome comprised the chromosome, seven plasmids and one linear phage-plasmid. Four carbapenemase genes were detected: bla NDM-5 and two copies of bla OXA-181 in the chromosome, and a second copy of bla NDM-5 on an 84 kb IncFII plasmid. CG147 genomes carried a mean of 13 acquired resistance genes or mutations; 63 % carried a carbapenemase gene and 83 % harboured bla CTX-M. All CG147 genomes presented GyrA and ParC mutations and a common subtype I-E CRISPR-Cas system. ST392 and ST273 emerged in 2005 and 1995, respectively. ST147, the most represented phylogenetic branch, was itself divided into two main clades with distinct capsular loci: KL64 (74 %, DJ included, emerged in 1994 and disseminated worldwide, with carbapenemases varying among world regions) and KL10 (20 %, emerged in 2002, predominantly found in Asian countries, associated with carbapenemases NDM and OXA-48-like). Furthermore, subclades within ST147-KL64 differed at the yersiniabactin locus, OmpK35/K36 mutations, plasmid replicons and prophages. The absence of IncF plasmids in some subclades was associated with a possible activity of a CRISPR-Cas system. K. pneumoniae CG147 comprises pandrug-resistant or extensively resistant isolates, and carries multiple and diverse resistance genes and mobile genetic elements, including chromosomal bla NDM-5. Its emergence is being driven by the spread of several phylogenetic clades marked by their own genomic features and specific temporo–spatial dynamics. These findings highlight the need for precision surveillance strategies to limit the spread of particularly concerning CG147 subsets.

Multi-Drug and β-Lactam Resistance in Escherichia coli and Food-Borne Pathogens from Animals and Food in Portugal, 2014–2019

Animal and food sources are seen as a potential transmission pathway of antimicrobial resistance (AMR) to humans. The aim of this study is to describe Campylobacter, Salmonella, and commensal Escherichia coli multi-drug resistance (MDR) in the food chain between 2014 and 2019 in Portugal. AMR surveillance data from food-producing animals and food were assessed. MDR relative frequencies were estimated by bacterial genus and year. AMR profiles were created using observations of resistance to antimicrobial classes from each isolate. Antimicrobial susceptibility testing results were clustered using k-modes. Clusters were described by population, AMR classification, β-lactamases, sample stage, sample type, season, and year. Overall, MDR was more prevalent for E. coli, ranging from 74–90% in animal and 94–100% in food samples. MDR was found to be more widespread in resistance profiles that were common among E. coli and Salmonella isolates and in those exclusively observed for E. coli, frequently including (fluoro)quinolones and cephalosporins resistance. β-lactam resistance was observed around 75% to 3rd/4th-generation cephalosporins in E. coli. Clusters suggest an escalating MDR behaviour from farm to post-farm stages in all bacteria and that Salmonella (fluoro)quinolones resistance may be associated with broilers. These findings support policy and decision making to tackle MDR in farm and post-farm stages.

Drug susceptibility testing of Mycobacterium tuberculosis using next generation sequencing and Mykrobe software

Introduction. Mycobacterium tuberculosis is the causative agent of tuberculosis. Drug susceptibility testing is performed by phenotypic and molecular tests. Commonly used for phenotypic drug susceptibility testing is the automated BACTEC system in a liquid culture medium. Drug susceptibility by line probe molecular tests was introduced almost 15 years ago. Recently whole genome sequencing (WGS) analysis of M. tuberculosis strains demonstrated that genotyping of drug-resistance could be accurately performed. Several software tools were developed.Our study aimed to perform whole-genome sequencing on phenotypically confirmed multi-drug resistant (MDR) M. tuberculosis strains, to identify drug-resistant mutations and to compare whole-genome sequencing profiles with line probe assay and phenotypic results.Materials and methods. We performed analysis on 34 MDR M. tuberculosis Bulgarian strains. Phenotypic drug susceptibility testing was performed on the BACTEC system. For molecular testing of drug susceptibility to first- and second-line tuberculostatics, we applied line probe assay Geno Type MTBDR plus v.1.0 и Geno Type MTBDR sl v.1.0. Sequencing was performed on MiSeq. Generated FASTQ files were analyzed for known drugresistant mutations with the software platform Mykrobe v.0.8.1.Results. All three methods — phenotypic analysis using the BACTEC system, genetic analysis of strains applying the Geno Type test and Mykrobe software gave comparable sensitivity/resistance results for the studied strains. All phenotypically proven rifampicin and isoniazid-resistant strains were 100% confirmed using Mykrobe software. The C-15T mutation is a marker for isoniazid resistance in strains of the SIT41 spoligotype. We observed a 75% (21/28) agreement between BACTEC and Mykrobe for ethambutol resistance. Phenotypically, 87% (n = 27) of the strains are resistant to streptomycin, but only 59% (n = 19) are proven by Mykrobe software. Comparing phenotypic and genotypic resistance to ofloxacin, amikacin and kanamycin, we observed 100% coincidence of results.Conclusions. Whole-genome sequencing approach is relatively expensive and laborious but useful for detailed analysis such as epidemiological genotyping and molecular drug susceptibility testing.

Luteolin increases susceptibility to macrolides by inhibiting MsrA efflux pump in Trueperella pyogenes

Trueperella pyogenes (T. pyogenes) is an opportunistic pathogen associated with a variety of diseases in many domestic animals. Therapeutic treatment options for T. pyogenes infections are becoming limited due to antimicrobial resistance, in which efflux pumps play an important role. This study aims to evaluate the inhibitory activity of luteolin, a natural flavonoid, on the MsrA efflux pump and investigate its mechanism. The results of antimicrobial susceptibility testing indicated that the susceptibility of msrA-positive T. pyogenes isolates to six macrolides increased after luteolin treatment, while the susceptibility of msrA-negative isolates showed no change after luteolin treatment. It is suspected that luteolin may increase the susceptibility of T. pyogenes isolates by inhibiting MsrA activity. After 1/2 MIC luteolin treatment for 36 h, the transcription level of the msrA gene and the expression level of the MsrA protein decreased by 55.0–97.7% and 36.5–71.5%, respectively. The results of an affinity test showed that the equilibrium dissociation constant (KD) of luteolin and MsrA was 6.462 × 10–5 M, and hydrogen bonding was predominant in the interaction of luteolin and MsrA. Luteolin may inhibit the ATPase activity of the MsrA protein, resulting in its lack of an energy source. The current study illustrates the effect of luteolin on MsrA in T. pyogenes isolates and provides insight into the development of luteolin as an innovative agent in combating infections caused by antimicrobial-resistant bacteria.

Antimicrobial Susceptibility of Clinical Oral Isolates of Actinomyces spp.

Actinomyces species play an important role in the pathogenesis of oral diseases and infections. Susceptibility testing is not always routinely performed, and one may oversee a shift in resistance patterns. The aim of the study was to analyze the antimicrobial susceptibility of 100 well-identified clinical oral isolates of Actinomyces spp. against eight selected antimicrobial agents using the agar dilution (AD) and E-Test (ET) methods. We observed no to low resistance against penicillin, ampicillin-sulbactam, meropenem, clindamycin, linezolid and tigecycline (0–2% ET, 0% AD) but high levels of resistance to moxifloxacin (93% ET, 87% AD) and daptomycin (83% ET, 95% AD). The essential agreement of the two methods was very good for benzylpenicillin (EA 95%) and meropenem (EA 92%). The ET method was reliable for correctly categorizing susceptibility, in comparison with the reference method agar dilution, except for daptomycin (categorical agreement 87%). Penicillin is still the first-choice antibiotic for therapy of diseases caused by Actinomyces spp.