Inconsistency of phenotypic and genomic characteristics of Campylobacter fetus subspecies requires reevaluation of current diagnostics.

Classifications of the Campylobacter fetus subspecies fetus and venerealis were first described in 1959 and were based on the source of isolation (intestinal versus genital) and the ability of the strains to proliferate in the genital tract of cows. Two phenotypic assays (1% glycine tolerance and H2S production) were described to differentiate the subspecies. Multiple molecular assays have been applied to differentiate the C. fetus subspecies, but none of these tests is consistent with the phenotypic identification methods. In this study, we defined the core genome and accessory genes of C. fetus, which are based on the closed genomes of five C. fetus strains. Phylogenetic analysis of the core genomes of 23 C. fetus strains of the two subspecies showed a division into two clusters. The phylogenetic core genome clusters were not consistent with the phenotypic classifications of the C. fetus subspecies. However, they were consistent with the molecular characteristics of the strains, which were determined by multilocus sequence typing, sap typing, and the presence/absence of insertion sequences and a type I restriction modification system. The similarity of the genome characteristics of three of the phenotypically defined C. fetus subsp. fetus strains to C. fetus subsp. venerealis strains, when considering the core genome and accessory genes, requires a critical evaluation of the clinical relevance of C. fetus subspecies identification by phenotypic assays.

First Closed Genome Sequence of Campylobacter fetus subsp. venerealis bv. intermedius.

Campylobacter fetus subsp. venerealis bv. intermedius is a variant of C. fetus subsp. venerealis, the causative agent of bovine genital campylobacteriosis, a venereal disease associated with abortion and infertility in cattle. We report the first closed whole-genome sequence of this biovar.

Extended-spectrum ß-lactamase-producing Escherichia coli from retail chicken meat and humans: comparison of strains, plasmids, resistance genes, and virulence factors.

BACKGROUND: The worldwide prevalence of extended-spectrum ß-lactamase (ESBL)-producing Enterobacteriaceae is increasing rapidly both in hospitals and in the community. A connection between ESBL-producing bacteria in food animals, retail meat, and humans has been suggested. We previously reported on the genetic composition of a collection of ESBL-producing Escherichia coli (ESBL-EC) from chicken meat and humans from a restricted geographic area. Now, we have extended the analysis with plasmid replicons, virulence factors, and highly discriminatory genomic profiling methods. METHODS: One hundred forty-five ESBL-EC isolates from retail chicken meat, human rectal carriers, and blood cultures were analyzed using multilocus sequence typing, phylotyping, ESBL genes, plasmid replicons, virulence genes, amplified fragment length polymorphism (AFLP), and pulsed-field gel electrophoresis (PFGE). RESULTS: Three source groups overlapped substantially when their genetic composition was compared. A combined analysis using all variables yielded the highest resolution (Wilks lambda [Λ]: 0.08). Still, a prediction model based on the combined data classified 40% of the human isolates as chicken meat isolates. AFLP and PFGE showed that the isolates from humans and chicken meat could not be segregated and identified 1 perfect match between humans and chicken meat. CONCLUSIONS: We found significant genetic similarities among ESBL-EC isolates from chicken meat and humans according to mobile resistance elements, virulence genes, and genomic backbone. Therefore, chicken meat is a likely contributor to the recent emergence of ESBL-EC in human infections in the study region. This raises serious food safety questions regarding the abundant presence of ESBL-EC in chicken meat.

Extended-spectrum ß-lactamase genes of Escherichia coli in chicken meat and humans, The Netherlands.

We determined the prevalence and characteristics of extended-spectrum ß-lactamase (ESBL) genes of Enterobacteriaceae in retail chicken meat and humans in the Netherlands. Raw meat samples were obtained, and simultaneous cross-sectional surveys of fecal carriage were performed in 4 hospitals in the same area. Human blood cultures from these hospitals that contained ESBL genes were included. A high prevalence of ESBL genes was found in chicken meat (79.8%). Genetic analysis showed that the predominant ESBL genes in chicken meat and human rectal swab specimens were identical. These genes were also frequently found in human blood culture isolates. Typing results of Escherichia coli strains showed a high degree of similarity with strains from meat and humans. These findings suggest that the abundant presence of ESBL genes in the food chain may have a profound effect on future treatment options for a wide range of infections caused by gram-negative bacteria.

New diagnostic microarray (Check-KPC ESBL) for detection and identification of extended-spectrum beta-lactamases in highly resistant Enterobacteriaceae.

The performance of a microarray for the detection of extended-spectrum beta-lactamases was determined on a collection of 638 highly resistant members of the family Enterobacteriaceae collected from patients in 18 hospitals in The Netherlands. The microarray had a significantly higher specificity than the phenotypic assays. It also detects carbapenemases and characterizes the resistance genes, providing epidemiological insight.

Abiotrophia defectiva infection of a total hip arthroplasty diagnosed by 16S rRNA gene sequencing.

We describe a case of a total hip arthroplasty infection caused by Abiotrophia defectiva, identified by 16S rRNA gene sequencing. Removal of the prosthesis followed by antibiotic treatment resulted in a good clinical outcome. 16S rRNA gene sequencing can be a useful tool in diagnosing infection with this fastidious microorganism that can easily be misidentified using phenotypic identification methods.

Phylogenetic variation of Aggregatibacter actinomycetemcomitans serotype e reveals an aberrant distinct evolutionary stable lineage.

The periodontal pathogen Aggregatibacter actinomycetemcomitans that comprises six serotypes (a-f), is often identified by PCR-based techniques targeting the 16S rRNA gene. In this study, 16S rRNA gene sequence analysis revealed an aberrant cluster of 19 strains within serotype e, denoted as serotype e'. The 16S rRNA gene sequence similarities found between serotype e' strains ranged from 99.7% to 100.0%, whereas 96.8-97.5% sequence similarity was obtained with members of the other serotypes, indicating that the serotype e' strains might not be true members of A. actinomycetemcomitans. However, DNA-DNA hybridizations between a representative serotype e' strain and representative strains of serotypes b, d and e of A. actinomycetemcomitans revealed 68-75% DNA-DNA relatedness, demonstrating that the serotype e' strains do belong to the species A. actinomycetemcomitans. AFLP analysis of 33 A. actinomycetemcomitans strains, representing all serotypes (a-f), but mainly serotype e' strains, showed that the latter form a distinct cluster, demonstrating that these strains are also closely related on the whole genome level. Moreover, the serotype e' strains were unable to ferment starch and glycogen in contrast to almost all other A. actinomycetemcomitans strains tested. Overall, the data obtained in this study suggest that the serotype e' strains form an evolutionary relatively stable distinct subgroup within A. actinomycetemcomitans.

Characterisation of carbapenem-resistant Acinetobacter baumannii outbreak strains producing OXA-58 in Turkey.

The aim of this study was to characterise the molecular epidemiology and mechanisms of carbapenem resistance of nosocomial Acinetobacter baumannii isolates in a new university hospital in Turkey. A total of 145 carbapenem-resistant A. baumannii (CRAB) isolates were collected during the period 2003-2006. All isolates were typed by amplified fragment length polymorphism (AFLP) analysis. AFLP analysis showed three predominant clusters consisting of 72, 20 and 12 clinical strains as well as some smaller clusters and 23 unique strains. The three main clonal AFLP types corresponded to three major antibiotic susceptibility patterns. One environmental isolate was found related to the major outbreak clone. The reference type strains of European clones I, II and III were also typed by AFLP and analysed for clonal similarity. Polymerase chain reaction (PCR) analysis of different carbapenem resistance genes showed that strains from each of the three main clusters as well as 79% of the remaining strains harboured the bla(OXA-58) gene. No genes encoding the metallo-beta-lactamases GIM-1, SIM-1, SPM-1, IMP-like and VIM-like or the oxacillinases OXA-24-like and OXA-23-like were detected. In conclusion, multiple clones of CRAB strains producing OXA-58-type oxacillinase were responsible for a sustained CRAB outbreak occurring in a hospital in Turkey. These isolates were not associated with A. baumannii strains of the major European clones I, II or III.

Clonal stability of Porphyromonas gingivalis in untreated periodontitis.

OBJECTIVES: The objective of the present investigation was to study the clonal stability of Porphyromonas gingivalis in a population of Indonesian subjects, deprived of dental care and with varying degrees of periodontitis over a period of 8 years. MATERIAL AND METHODS: In 1994, 105 subjects and in 2002, 103 subjects were P. gingivalis culture positive. Multiple isolates from each of these subjects were used for amplified fragment length polymorphism (AFLP) typing. RESULTS: Sixty-six individuals were P. gingivalis culture positive at both time points. In 31 subjects (47%) an exact identical P. gingivalis genotype distribution was found in 1994 and in 2002. In 26 of these subjects one genotype, in eight subjects two identical genotypes were found at both time points. In 70% of the subjects at least one P. gingivalis genotype was found in 1994 and 2002, whereas other genotypes were either newly detected or were no longer detectable. Identical genotypes were found in 26% of the sibships. Clonal stability in siblings was 39%. Horizontal transmission of P. gingivalis was only found in 2002 and was low (11%). In total, 56 P. gingivalis genotypes were identified in 1994 and 61 in 2002. Twenty-four appeared unique, whereas other genotypes were found in multiple subjects within as well as without families. One genotype occurred in 11 different subjects. CONCLUSIONS: The clonal stability of P. gingivalis under natural conditions is high. Complete different genotype distribution was found in only 27% of the subjects. Transmission of P. gingivalis occurred frequently among siblings but not among spouses.

Extended-spectrum-beta-lactamase production in a Salmonella enterica serotype Typhi strain from the Philippines.

A Salmonella enterica serotype Typhi strain was cultured from blood and fecal samples from a 54-year-old man with fever and diarrhea. He had returned from travel to the Philippines a few days earlier. Phenotypic and genotypic analysis confirmed the production of the SHV-12 extended-spectrum beta-lactamase.