The prevalence of resistance genes in two important anaerobic genera, Bacteroides and Prevotella, was assessed by applying PCR specifically directed to genes of interest.
A total of 101 Bacteroides ...spp. and 99 Prevotella spp. human clinical isolates were identified using MALDI-TOF MS. The presence of the resistance genes cfxA, cepA, cfiA, tetQ, ermF and nim, was assessed. Prevalence of resistance genes was compared with the phenotypic resistance against amoxicillin, clindamycin, meropenem and metronidazole.
Even though the majority of the Bacteroides isolates (95.0%) showed resistance towards amoxicillin, only 52/101 of the isolates harboured one of the resistance genes, accounting for this resistance. Within the genus Prevotella the presence of cfxA (50/99) almost perfectly matched the amoxicillin resistance (48/99). No difference in prevalence of the ermF gene (16/101 and 9/99) and clindamycin resistance (16/101 and 10/99) was observed within Bacteroides and Prevotella, respectively. Two isolates of Prevotella were resistant to metronidazole. One harboured the nim gene. One metronidazole-susceptible isolate of Bacteroides harboured a nim gene. Within the Bacteroides and Prevotella genera, 6/101 strains and 5/99 isolates harboured three different resistance genes, respectively, among them tetQ. TetQ is often located on a conjugative transposon, increasing the chance of horizontal gene transfer between isolates.
An unknown mechanism in Bacteroides non-fragilis isolates causes resistance to β-lactam antibiotics. The fact that the prevalence of the tetQ gene among Prevotella is increasing and the existence of isolates harbouring three resistance genes are worrisome developments.
Abstract The glycopeptide avoparcin, bacitracin, the macrolides spiramycin and tylosin, and the streptogramin virginiamycin were withdrawn as growth promoters in the European Union between 1995 and ...1999 on the basis of the Precautionary Principle. Relevant resistance thereupon diminished among enterococci (the indicator organisms) isolated from animal and human faeces. However, animal enterococci were shown to differ from those that caused human infections, although their resistance genes were sometimes indistinguishable and thus probably have a common origin. Before the ban, human clinical isolates of enterococci resistant to vancomycin or teicoplanin were uncommon in many, but not all, parts of Europe and resistance to quinupristin/dalfopristin in the case of Enterococcus faecium was very rare. After the ban, these resistances increased in prevalence almost universally, to the detriment of human health. Campylobacters, normally susceptible to macrolides, increased in prevalence before and after the ban. Analyses suggest that the added risk to human health from resistance among enterococci and campylobacters selected by growth promoter use is small, whilst the benefit to human health from their use, hitherto largely ignored, might more than counterbalance this.
Abstract This work investigates the occurrence and features of class 1 integrons and the presence of transferable quinolone resistance determinants (TQRD) among 382 clinical Salmonella enterica ...isolates of non-Typhimurium serotypes as well as the β-lactamases produced by amoxicillin-resistant isolates. These isolates were recovered in 2001 and from 2004 to 2009 from patients from the health region of Terres de l’Ebre (Catalonia, Spain) and comprised 41 different serotypes, mostly of serovar Enteritidis ( n = 272), being 16.5% multidrug-resistant (MDR). Among the 93 amoxicillin-resistant isolates, 84 produced TEM-1,4 produced an extended-spectrum β-lactamase (CTX-M-9 in one S. Grumpensis and in one S. Virchow, CTX-M-15 in S. Kapemba, and SHV-12 in S. Enteritidis), one produced DHA-1 ( S. Newport), and 4 did not present any of the investigated β-lactamases. TQRD were found in 2 isolates ( qnrA1 in CTX-M-9-producing S. Grumpensis and qnrB4 in DHA-1-producing S. Newport). Overall, 35 isolates (9.2% of all isolates and 54% of MDR isolates) belonging to 15 different serotypes carried class 1 integrons that were transferred by conjugation in 17 isolates. Eleven distinct cassette arrangements were identified, with dfrA1-aadA1 , dfrA17-aadA5 , and dfrA12-orfF-aadA2 being the most prevalent and widely distributed ones. Atypical sul3 -associated integrons were detected in 5 isolates of serotypes Rissen and Enteritidis. Moreover, the presence of integrons in the serotypes Kapemba, Mikawasima, and 9,12:Iv:i:-, of the estX-psp (linked to sul3 ) and aadA13-sat cassette arrangements in S. enterica , of extended-spectrum β-lactamases in S. Kapemba and S. Grumpensis, and of TQRD in S. Grumpensis is reported here for the first time.
Aims: The aims of this study were to characterize the molecular variations in the quinolone resistance-determining region (QRDR) of gyrA among quinolone-resistant and -susceptible Campylobacter ...jejuni isolates originating from foods of animal origin and human infections and to evaluate the suitability of the single-strand conformation polymorphism (SSCP) method as a screening method for molecular characterization of fluoroquinolone resistance. Methods and Results: Alterations in QRDR of gyrA from 182 C. jejuni isolates were determined by nonradioisotopic SSCP analysis and direct sequencing. A total of 13 types of nucleic acid sequence combinations within the QRDR of the gyrA gene resulted in 11 different SSCP patterns. All nalidixic acid resistant strains possessed nucleotide substitution at either codon Thr-86 or Asp-90. Silent mutations were detected additionally. Thr-86 to Ile mutation was detected in all 139 ciprofloxacin resistant strains, which showed cross-resistance to nalidixic acid. Conclusions: The SSCP method is suitable for a molecular screening of quinolone resistant C. jejuni isolates and in combination with DNA sequencing suitable to detect genetic variations of the QRDR of gyrA. Significance and Impact of Study: This study provides data of the genetic variations of the QRDR of gyrA from C. jejuni isolates of foods and human beings.
Fungi host viruses from many families, and next-generation sequencing can be used to discover previously unknown genomes. Some fungus-infecting viruses (mycoviruses) confer hypovirulence on their ...pathogenic hosts, raising the possibility of therapeutic application in the treatment of fungal diseases. Though all fungi probably host mycoviruses, many human pathogens have none documented, implying the mycoviral catalogue remains at an early stage. Here, we carried out virus discovery on 61 cultures of pathogenic fungi covering 27 genera and at least 56 species. Using next-generation sequencing of total nucleic acids, we found no DNA viruses but did find a surprising RNA virus diversity of 11 genomes from six classified families and two unclassified lineages, including eight genomes likely representing new species. Among these was the first jivivirus detected in a fungal host (Aspergillus lentulus). We separately utilized rolling circle amplification and next-generation sequencing to identify ssDNA viruses specifically. We identified 13 new cressdnaviruses across all libraries, but unlike the RNA viruses, they could not be confirmed by PCR in either the original unamplified samples or freshly amplified nucleic acids. Their distributions among sequencing libraries and inconsistent detection suggest low-level contamination of reagents. This highlights both the importance of validation assays and the risks of viral host prediction on the basis of highly amplified sequencing libraries. Meanwhile, the detected RNA viruses provide a basis for experimentation to characterize possible hypovirulent effects, and hint at a wealth of uncharted viral diversity currently frozen in biobanks.
Fungal pathogens of humans are a growing global health burden. Viruses of fungi may represent future therapeutic tools, but for many fungal pathogens there are no known viruses. Our study examined the viral content of diverse human-pathogenic fungi in a clinical biobank, identifying numerous viral genomes, including one lineage previously not known to infect fungi.
Genetic variation at the genome level, and consequently phylogenetic relationship, has been well studied in the closely related human pathogens Yersinia pseudotuberculosis and Yersinia pestis. In ...contrast the remaining pathogenic species of the genus, Yersinia enterocolitica is relatively poorly understood, with only one genome sequence available from a biotype of the species rarely isolated from humans or animals worldwide. In this study we present a reference genome sequence for each of the Y. enterocolitica biotypes, and discuss comparative genomics across the species. In addition we also present phylogenetic data for the species, and its position with the wider genus, based on genome sequences of 100 Y. enterocolitica strains. The study provides new and exciting insights into the evolution of pathogenesis in the Yersinia genus, and in particular of the Y. enterocolitica species.
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