High prevalence of inducible erythromycin resistance among Streptococcus bovis isolates in Taiwan

Genomic insights into plasmid-mediated antimicrobial resistance in the bacterium Bhargavaea beijingensis strain PS04

The dissemination of antimicrobial-resistant bacteria through environment is a major health concern for public health. Pathogenic bacteria in natural environment can mediate the transfer of antimicrobial-resistant genes via horizontal gene transfer to naturally occurring bacteria in the soil. Bhargavaea beijingensis is a Gram-negative bacterium that is commonly found in soil and water. In recent years, there has been an emergence of antibiotic-resistant strains of environmental bacteria, which pose a significant threat to human health. One mechanism of antibiotic resistance in bacteria is through the acquisition of plasmids, which can carry genes that confer resistance to various antibiotics. In this study, a novel plasmid of repUS12 replicon type was identified in the strain PS04 of B. beijingensis, which carried the ermT and tet(L) genes, encoding resistance to macrolides, lincosamides, and tetracycline. The plasmid was found to be the first of its kind in B. beijingensis and was thought to have been acquired through horizontal gene transfer. The emergence of plasmid-mediated resistance in B. beijingensis highlights the need for continued surveillance and monitoring of antibiotic resistance in environmental bacteria.

Phenotypic and Genotypic Characterization of Antimicrobial Resistance in Streptococci Isolated from Human and Animal Clinical Specimens

Recently, the phenomenon of infection of humans as hosts by animal pathogens has been increasing. Streptococcus is an example of a genus in which bacteria overcome the species barrier. Therefore, monitoring infections caused by new species of human pathogens is critical to their spread. Seventy-five isolates belonging to streptococcal species that have recently been reported as a cause of human infections with varying frequency, were tested. The aim of the study was to determine the drug resistance profiles of the tested strains, the occurrence of resistance genes and genes encoding the most important streptococcal virulence factors. All tested isolates retained sensitivity to β-lactam antibiotics. Resistance to tetracyclines occurred in 56% of the tested strains. We have detected the MLS_B type resistance (cross-resistance to macrolide, lincosamide, and streptogramin B) in 20% of the tested strains. 99% of the strains had tetracycline resistance genes. The erm class genes encoding MLS_B resistance were present in 47% of strains. Among the strains with MLS_B resistance, 92% had the streptokinase gene, 58% the streptolysin O gene and 33% the streptolysin S gene. The most extensive resistance concerned isolates that accumulated the most traits and genes, both resistance genes and virulence genes, increasing their pathogenic potential. Among the tested strains, the gene encoding streptokinase was the most common. The results of the prove that bacteria of the species S. uberis, S. dysgalactiae and S. gallolyticus are characterized by a high pathogenic potential and can pose a significant threat in case of infection of the human body.

Comparative Evaluation of Current Biochemical-, Sequencing-, and Proteomic-Based Identification Methods for the Streptococcus bovis Group

The Streptococcus bovis group (previously group D streptococci) consists of seven distinct species and subspecies. Definitive identification within the group is important, as certain organisms have been associated with gastrointestinal carcinoma, bacteremia, infective endocarditis, meningitis, biliary tract disease, and carcinoma, among others. Definitive identification, however, remains elusive due to limitations and inconsistencies across commonly used identification platforms in the United States. Here, we compared the performance of standard biochemical (Trek Gram-positive identification [GPID] plate, Vitek 2 GPID), sequencing (16S rDNA, sodA) databases (NCBI, RDP, CDC MicrobeNet), and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) platforms (Vitek MS, Bruker Biotyper MS) using a set of eight type strains representing all seven strains within the S. bovis group. Despite the evaluation of contemporary methods, no single platform was able to definitively identify all type strains within the S. bovis group. Vitek MS (85.7%, 7/8) provided the most accurate definitive identifications, followed by sodA sequencing (75%, 6/8). Vitek 2 and Bruker Biotyper RUO platforms performed the next best (62.5%, 5/8). All remaining platforms failed to adequately differentiate type strains within the S. bovis group (range, 0 to 37.5%). Laboratorians and clinicians should be aware of the identification limitations of routine testing algorithms and incorporate reflex testing, when appropriate, to platforms such as Vitek MS and/or sodA sequencing that are more able to definitively identify S. bovis group organisms. Further clinical evaluation was conducted using 65 clinical isolates from three geographically distinct U.S. institutions. Future improvements in identification platforms may reveal new clinical and epidemiological trends for members of the S. bovis group.

Diversity and Antimicrobial Resistance in the Streptococcus bovis/Streptococcus equinus Complex (SBSEC) Isolated from Korean Domestic Ruminants

S. bovis/S. equinus complex (SBSEC) includes lactic acid-producing bacteria considered as the causative agent associated with acute rumen lactic acidosis in intensive ruminants. Considering the limited information on the detailed characteristics and diversity of SBSEC in Korea and the emergence of antimicrobial resistance (AMR), we investigated the diversity of SBSEC from domestic ruminants and verified the presence of antimicrobial resistance genes (ARGs) against several antimicrobials with their phenotypic resistance. Among 51 SBSEC isolates collected, two SBSEC members (S. equinus and S. lutetiensis) were identified; sodA-based phylogenetic analyses and comparisons of overall genome relatedness revealed potential plasticity and diversity. The AMR rates of these SBSEC against erythromycin, clindamycin, and tetracycline were relatively lower than those of other SBSEC isolates of a clinical origin. An investigation of the ARGs against those antimicrobials indicated that tetracycline resistance of SBSECs generally correlated with the presence of tet(M)-possessing Tn916-like transposon. However, no correlation between the presence of ARGs and phenotypic resistance to erythromycin and clindamycin was observed. Although a limited number of animals and their SBSEC isolates were examined, this study provides insights into the potential intraspecies biodiversity of ruminant-origin SBSEC and the current status on antimicrobial resistance of the bacteria in the Korean livestock industry.

Diversity and Antimicrobial Resistance in the Streptococcus bovis/Streptococcus equinus Complex (SBSEC) Isolated from Korean Domestic Ruminants

S. bovis/S. equinus complex (SBSEC) includes lactic acid-producing bacteria considered as the causative agent associated with acute rumen lactic acidosis in intensive ruminants. Considering the limited information on the detailed characteristics and diversity of SBSEC in Korea and the emergence of antimicrobial resistance (AMR), we investigated the diversity of SBSEC from domestic ruminants and verified the presence of antimicrobial resistance genes (ARGs) against several antimicrobials with their phenotypic resistance. Among 51 SBSEC isolates collected, two SBSEC members (S. equinus and S. lutetiensis) were identified; sodA-based phylogenetic analyses and comparisons of overall genome relatedness revealed potential plasticity and diversity. The AMR rates of these SBSEC against erythromycin, clindamycin, and tetracycline were relatively lower than those of other SBSEC isolates of a clinical origin. An investigation of the ARGs against those antimicrobials indicated that tetracycline resistance of SBSECs generally correlated with the presence of tet(M)-possessing Tn916-like transposon. However, no correlation between the presence of ARGs and phenotypic resistance to erythromycin and clindamycin was observed. Although a limited number of animals and their SBSEC isolates were examined, this study provides insights into the potential intraspecies biodiversity of ruminant-origin SBSEC and the current status on antimicrobial resistance of the bacteria in the Korean livestock industry.

Diversity and Antimicrobial Resistance in the Streptococcus bovis/Streptococcus equinus Complex (SBSEC) Isolated from Korean Domestic Ruminants

S. bovis/S. equinus complex (SBSEC) includes lactic acid-producing bacteria considered as the causative agent associated with acute rumen lactic acidosis in intensive ruminants. Considering the limited information on the detailed characteristics and diversity of SBSEC in Korea and the emergence of antimicrobial resistance (AMR), we investigated the diversity of SBSEC from domestic ruminants and verified the presence of antimicrobial resistance genes (ARGs) against several antimicrobials with their phenotypic resistance. Among 51 SBSEC isolates collected, two SBSEC members (S. equinus and S. lutetiensis) were identified; sodA-based phylogenetic analyses and comparisons of overall genome relatedness revealed potential plasticity and diversity. The AMR rates of these SBSEC against erythromycin, clindamycin, and tetracycline were relatively lower than those of other SBSEC isolates of a clinical origin. An investigation of the ARGs against those antimicrobials indicated that tetracycline resistance of SBSECs generally correlated with the presence of tet(M)-possessing Tn916-like transposon. However, no correlation between the presence of ARGs and phenotypic resistance to erythromycin and clindamycin was observed. Although a limited number of animals and their SBSEC isolates were examined, this study provides insights into the potential intraspecies biodiversity of ruminant-origin SBSEC and the current status on antimicrobial resistance of the bacteria in the Korean livestock industry.

Microbiological and clinical characteristics of Streptococcus gallolyticus subsp. pasteurianus infection in China

BACKGROUND

Infections by Streptococcus gallolyticus subsp. pasteurianus (SGSP) is often underestimated. Herein, the epidemiological features and resistant characteristics of SGSP in mainland China are characterized to enable a better understanding of its role in clinical infections.

METHODS

In the present work, 45 SGSP isolates were collected from the samples of bloodstream, urine, aseptic body fluid, and fetal membrane/placenta from patients in 8 tertiary general hospitals of 6 cities/provinces in China from 2011 to 2017. The identification of all isolates was performed using traditional biochemical methods, 16S rRNA and gyrB sequencing, followed by the characterization of their antibiotic resistance profiling and involved genes.

RESULTS

Among 34 non-pregnancy-related patients, 4 (4/34,11.8%) patients had gastrointestinal cancer, 10 (10/34, 29.4%) patients had diabetes, and one patient had infective endocarditis. Moreover, 11 cases of pregnant women were associated with intrauterine infection (9/11, 81.2%) and urinary tract infection (1/11, 9.1%), respectively. Except one, all other SGSP isolates were correctly identified by the BD Phoenix automated system. We found that all SGSP isolates were phenotypically susceptible to penicillin, ampicillin, cefotaxime, meropenem, and vancomycin. Forty strains (40/45, 88.9%) were both erythromycin and clindamycin-resistant, belonging to the cMLS_B phenotype, and the majority of them carried erm(B) gene (39/40, 97.5%). Although the cMLS_B/erm(B) constituted the most frequently identified phenotype/genotype combination (25/40, 62.5%) among all erythromycin-resistant cMLS_B isolates, erm(B)/erm(A), erm(B)/mef(A/E), and erm(B)/erm(T) was detected in 7, 4, and 3 isolates, respectively. Furthermore, 43 strains (43/45, 95.6%) were tetracycline-resistant, and out of these, 39 strains (39/45, 86.7%) carried tet(L), 27(27/45, 60.0%) strains carried tet(O), and 7 (7/45, 15.6%) strains carried tet(M), alone or combined, respectively. All erythromycin-resistant isolates were also resistant to tetracycline.

CONCLUSIONS

It is important to study and draw attention on SGSP, an underreported opportunistic pathogen targeting immunodeficient populations, notably elderly subjects, pregnant women and neonates.

The characteristics of gut microbiota and commensal Enterobacteriaceae isolates in tree shrew (Tupaia belangeri)

BACKGROUND

Tree shrew is a novel laboratory animal with specific characters for human disease researches in recent years. However, little is known about its characteristics of gut microbial community and intestinal commensal bacteria. In this study, 16S rRNA sequencing method was used to illustrate the gut microbiota structure and commensal Enterobacteriaceae bacteria were isolated to demonstrate their features.

RESULTS

The results showed Epsilonbacteraeota (30%), Proteobacteria (25%), Firmicutes (19%), Fusobacteria (13%), and Bacteroidetes (8%) were the most abundant phyla in the gut of tree shrew. Campylobacteria, Campylobacterales, Helicobacteraceae and Helicobacter were the predominant abundance for class, order, family and genus levels respectively. The alpha diversity analysis showed statistical significance (P < 0.05) for operational taxonomic units (OTUs), the richness estimates, and diversity indices for age groups of tree shrew. Beta diversity revealed the significant difference (P < 0.05) between age groups, which showed high abundance of Epsilonbacteraeota and Spirochaetes in infant group, Proteobacteria in young group, Fusobacteria in middle group, and Firmicutes in senile group. The diversity of microbial community was increased followed by the aging process of this animal. 16S rRNA gene functional prediction indicated that highly hot spots for infectious diseases, and neurodegenerative diseases in low age group of tree shrew (infant and young). The most isolated commensal Enterobacteriaceae bacteria from tree shrew were Proteus spp. (67%) and Escherichia coli (25%). Among these strains, the antibiotic resistant isolates were commonly found, and pulsed-field gel electrophoresis (PFGE) results of Proteus spp. indicated a high degree of similarity between isolates in the same age group, which was not observed for other bacteria.

CONCLUSIONS

In general, this study made understandings of the gut community structure and diversity of tree shrew.

An Overview on Streptococcus bovis/Streptococcus equinus Complex Isolates: Identification to the Species/Subspecies Level and Antibiotic Resistance

Streptococcus bovis/Streptococcus equinus complex (SBSEC), a non-enterococcal group D Streptococcus spp. complex, has been described as commensal bacteria in humans and animals, with a fecal carriage rate in humans varying from 5% to over 60%. Among streptococci, SBSEC isolates represent the most antibiotic-resistant species—with variable resistance rates reported for clindamycin, erythromycin, tetracycline, and levofloxacin—and might act as a reservoir of multiple acquired genes. Moreover, reduced susceptibility to penicillin and vancomycin associated with mobile genetic elements have also been detected, although rarely. Since the association of SBSEC bacteremia and colon lesions, infective endocarditis and hepatobiliary diseases has been established, particularly in elderly individuals, an accurate identification of SBSEC isolates to the species and subspecies level, as well as the evaluation of antibiotic resistance, are needed. In this paper, we reviewed the major methods used to identify SBSEC isolates and the antimicrobial resistance rates reported in the scientific literature among SBSEC species.

Identification, antimicrobial resistance and molecular characterization of the human emerging pathogen Streptococcus gallolyticus subsp. pasteurianus

This study aimed to retrospectively identify 22Streptococcus bovis clinical strains based on the new taxonomy, as well as to investigate their antibiotic-resistance and clonality. Strains were identified by Phoenix100 system, 16S rRNA sequencing, and two MALDI-TOF MS platforms (Bruker Biotyper, Vitek MS). Antibiotic resistance was determined both phenotypically and genotypically, and clonality was assessed by PFGE. Most of strains (63.6%) were isolated from urine, and diabetes was the most common underlying disease (31.8%). Phoenix100 system revealed all strains belonged to biotype II, and 16S rRNA sequencing identified all strains as S. gallolyticus subsp pasteurianus (SGSP). Although both MALDI-TOF MS systems correctly identified isolates to the species level, only Bruker Biotyper accurately identified to the subspecies level. Erythromycin-resistant strains (31.8%) were also clindamycin-resistant and positive for erm(B). Strains resistant to tetracycline (68.2%) were also resistant to erythromycin. PFGE showed high genetic variability identifying 17 different pulsotypes, most of which single.

Inducible Expression of both ermB and ermT Conferred High Macrolide Resistance in Streptococcus gallolyticus subsp. pasteurianus Isolates in China

Streptococcus gallolyticus subsp. pasteurianus is an under-recognized pathogen and zoonotic agent causing opportunistic infections in humans. Despite increasing recognition of this subspecies as a cause for human infectious diseases, limited information is known about its antibiotic resistance mechanism. In this study, we aim to identify the molecular mechanism underlying the high macrolide resistance of six S. gallolyticus subsp. pasteurianus isolates from dead ducklings collected in several natural outbreaks in China during 2010–2013. All isolates exhibited multi-drug resistance including high macrolide resistance (MIC ≥ 1024 mg/L for erythromycin, and 512 mg/L for clarithromycin). Efflux-encoding mefA and mefE genes were not detectable in these isolates. The presence of 23S rRNA mutations in specific isolates did not significantly change macrolide MICs. No nucleotide substitutions were found in genes encoding ribosomal proteins L4 or L22. The ermB and ermT genes were found in the genomes of all isolates. These two genes were acquired independently in one highly virulent isolate AL101002, and clustered with Tn916 and IS1216, respectively. The expression of both ermB and ermT in all isolates was erythromycin inducible and yielded comparable macrolide MICs in all six isolates. Taken together, inducible expression of both ermB and ermT conferred high macrolide resistance in these S. gallolyticus subsp. pasterianus isolates. Our findings reveal new macrolide resistance features in S. gallolyticus subsp. pasteurianus by both ermB and ermT.

Antibiotic resistance genes and human bacterial pathogens: Co-occurrence, removal, and enrichment in municipal sewage sludge digesters

Understanding which/how antibiotic resistance genes (ARGs) contribute to increased acquisition of resistance by pathogens in aquatic environments are challenges of profound significance. We explored the co-occurrence and removal versus enrichment of ARGs and human bacterial pathogens (HBPs) in municipal sewage sludge digesters. We combined metagenomic detection of a wide spectrum of 323 ARGs and 83 HBPs with a correlation-based statistical approach and charted a network of their co-occurrence relationships. The results indicate that most ARGs and a minor proportion of HBPs (mainly Collinsella aerofaciens, Streptococcus salivarius and Gordonia bronchialis) could not be removed by anaerobic digestion, revealing a biological risk of post-digestion sludge in disseminating antibiotic resistance and pathogenicity. Moreover, preferential co-occurrence patterns were evident within one ARG type (e.g., multidrug, beta-lactam, and aminoglycoside) and between two different ARG types (i.e., aminoglycoside and beta-lactam), possibly implicating co-effects of antibiotic selection pressure and co-resistance on shaping antibiotic resistome in sewage sludge. Unlike beta-lactam resistance genes, ARGs of multidrug and macrolide-lincosamide-streptogramin tended to co-occur more with HBPs. Strikingly, we presented evidence that the most straightforward biological origin of an ARG-species co-occurring event is a hosting relationship. Furthermore, a significant and robust HBP-species co-occurrence correlation provides a proper scenario for nominating HBP indicators (e.g., Bifidobacterium spp. are perfect indicators of C. aerofaciens; r = 0.92-0.99 and P-values < 0.01). Combined, this study demonstrates a creative and effective network-based metagenomic approach for exploring ARG hosts and HBP indicators and assessing ARGs acquisition by HBPs in human-impacted environments where ARGs and HBPs may co-thrive.

Draft Genome Sequence of Erythromycin-Resistant Streptococcus gallolyticus subsp. gallolyticus NTS 31106099 Isolated from a Patient with Infective Endocarditis and Colorectal Cancer

Streptococcus gallolyticus subsp. gallolyticus is known for its close association with infective endocarditis and colorectal cancer in humans. Here, we report the draft genome sequence of highly erythromycin-resistant strain NTS 31106099 isolated from a patient with infective endocarditis and colorectal cancer.

A novel erythromycin resistance plasmid from Bacillus sp. strain HS24, isolated from the marine sponge Haliclona simulans

A better understanding of the origin and natural reservoirs of resistance determinants is fundamental to efficiently tackle antibiotic resistance. This paper reports the identification of a novel 5.8 kb erythromycin resistance plasmid, from Bacillus sp. HS24 isolated from the marine sponge Haliclona simulans. pBHS24B has a mosaic structure and carries the erythromycin resistance gene erm(T). This is the first report of an erythromycin resistance plasmid from a sponge associated bacteria and of the Erm(T) determinant in the genus Bacillus.

Genomics, evolution, and molecular epidemiology of the Streptococcus bovis/Streptococcus equinus complex (SBSEC)

The Streptococcus bovis/Streptococcus equinus complex (SBSEC) is a group of human and animal derived streptococci that are commensals (rumen and gastrointestinal tract), opportunistic pathogens or food fermentation associates. The classification of SBSEC has undergone massive changes and currently comprises 7 (sub)species grouped into four branches based on sequences identities: the Streptococcus gallolyticus, the Streptococcus equinus, the Streptococcus infantarius and the Streptococcus alactolyticus branch. In animals, SBSEC are causative agents for ruminal acidosis, potentially laminitis and infective endocarditis (IE). In humans, a strong association was established between bacteraemia, IE and colorectal cancer. Especially the SBSEC-species S. gallolyticus subsp. gallolyticus is an emerging pathogen for IE and prosthetic joint infections. S. gallolyticus subsp. pasteurianus and the S. infantarius branch are further associated with biliary and urinary tract infections. Knowledge on pathogenic mechanisms is so far limited to colonization factors such as pili and biofilm formation. Certain strain variants of S. gallolyticus subsp. macedonicus and S. infantarius subsp. infantarius are associated with traditional dairy and plant-based food fermentations and display traits suggesting safety. However, due to their close relationship to virulent strains, their use in food fermentation has to be critically assessed. Additionally, implementing accurate and up-to-date taxonomy is critical to enable appropriate treatment of patients and risk assessment of species and strains via recently developed multilocus sequence typing schemes to enable comparative global epidemiology. Comparative genomics revealed that SBSEC strains harbour genomics islands (GI) that seem acquired from other streptococci by horizontal gene transfer. In case of virulent strains these GI frequently encode putative virulence factors, in strains from food fermentation the GI encode functions that are pivotal for strain performance during fermentation. Comparative genomics is a powerful tool to identify acquired pathogenic functions, but there is still an urgent need for more physiological and epidemiological data to understand SBSEC-specific traits.

Molecular characterization of Streptococcus agalactiae isolates harboring small erm(T)-carrying plasmids

Among 1,827 group B Streptococcus (GBS) strains collected between 2006 and 2013 by the French National Reference Center for Streptococci, 490 (26.8%) strains were erythromycin resistant. The erm(T) resistance gene was found in six strains belonging to capsular polysaccharides Ia, III, and V and was carried by the same mobilizable plasmid, which could be efficiently transferred by mobilization to GBS and Enterococcus faecalis recipients, thus promoting a broad dissemination of erm(T).

Bacteraemia due to Streptococcus gallolyticus subspecies pasteurianus is associated with digestive tract malignancies and resistance to macrolides and clindamycin

OBJECTIVES

This study was intended to delineate the association between digestive tract malignancies and bacteraemia due to Streptococcus gallolyticus subspecies pasteurianus.

METHODS

We reviewed the medical records and microbiological results of patients with bacteraemia due to Streptococcus bovis during the period 2000-2012. Species and subspecies identification of isolates originally classified as S. bovis was confirmed by 16S rRNA sequencing and PCR restriction fragment length polymorphism (PCR-RFLP) assays. Minimum inhibitory concentrations of antimicrobial agents were determined by the broth microdilution method.

RESULTS

Of the 172 S. bovis complex isolates obtained from 172 patients (age range, <1-94 years, median age, 66) with bacteraemia, 31 isolates were identified to be S. gallolyticus subspecies gallolyticus, 126 were S. gallolyticus subspecies pasteurianus, and 15 were shown to be Streptococcus infantarius. The majority (n = 104, 60%) of patients were male and had underlying malignancies (n = 87, 51%). Bacteraemia due to S. gallolyticus subspecies gallolyticus was significantly associated with endocarditis while S. gallolyticus subspecies pasteurianus was more likely to be associated with malignancies of the digestive tract, including gastric, pancreatic, hepatobiliary and colorectal cancers. Septic shock at presentation was the only factor associated with mortality among patients with bacteraemia due to either subspecies of S. bovis. Isolates of S. gallolyticus subspecies pasteurianus had higher rates of resistance to macrolides and clindamycin than isolates of S. gallolyticus subspecies gallolyticus.

CONCLUSION

Extensive diagnostic work-up for digestive tract malignancies and trans-esophageal echocardiogram should be investigated in patients with bacteraemia caused by S. gallolyticus.

Novel erm(T)-carrying multiresistance plasmids from porcine and human isolates of methicillin-resistant Staphylococcus aureus ST398 that also harbor cadmium and copper resistance determinants

This study describes three novel erm(T)-carrying multiresistance plasmids that also harbor cadmium and copper resistance determinants. The plasmids, designated pUR1902, pUR2940, and pUR2941, were obtained from porcine and human methicillin-resistant Staphylococcus aureus (MRSA) of the clonal lineage ST398. In addition to the macrolide-lincosamide-streptogramin B (MLSB) resistance gene erm(T), all three plasmids also carry the tetracycline resistance gene tet(L). Furthermore, plasmid pUR2940 harbors the trimethoprim resistance gene dfrK and the MLSB resistance gene erm(C), while plasmids pUR1902 and pUR2941 possess the kanamycin/neomycin resistance gene aadD. Sequence analysis of approximately 18.1 kb of the erm(T)-flanking region from pUR1902, 20.0 kb from pUR2940, and 20.8 kb from pUR2941 revealed the presence of several copies of the recently described insertion sequence ISSau10, which is probably involved in the evolution of the respective plasmids. All plasmids carried a functional cadmium resistance operon with the genes cadD and cadX, in addition to the multicopper oxidase gene mco and the ATPase copper transport gene copA, which are involved in copper resistance. The comparative analysis of S. aureus RN4220 and the three S. aureus RN4220 transformants carrying plasmid pUR1902, pUR2940, or pUR2941 revealed an 8-fold increase in CdSO4 and a 2-fold increase in CuSO4 MICs. The emergence of multidrug resistance plasmids that also carry heavy metal resistance genes is alarming and requires further surveillance. The colocalization of antimicrobial resistance genes and genes that confer resistance to heavy metals may facilitate their persistence, coselection, and dissemination.

Bacterial community characteristics under long-term antibiotic selection pressures

To investigate bacterial community characteristics under long-term antibiotic selection pressures, water samples from the upstream and the downstream sections of two rivers individually receiving the treated penicillin G and oxytetracycline production wastewater, as well as the anaerobic and the aerobic effluent of the penicillin G production wastewater treatment plant, were taken and analyzed. Antibiotic resistance ratios of bacterial communities in water samples were estimated by culture-based analysis. The majority of bacterial colonies (approximately 55%-70%) in both downstream rivers and the aerobic effluent showed resistance to 80 μg/ml of antibiotics tested, while the resistance ratios were less than 10% and 5% respectively for both upstream rivers. Six 16S rRNA gene clone libraries were constructed with 355 sequences and 215 OTUs totally obtained representing 465 clones. The antibiotic stresses seemed not reduce the diversities of bacterial communities in antibiotic containing water samples compared to those in the two reference upstream rivers. Bacterial groups present in the two reference upstream rivers were common residents in freshwater ecosystems, with the dominant groups as the phyla Proteobacteria including Alphaproteobacteria, Betaproteobacteria and Gammaproteobacteria, as well as Actinobacteria and Bacteroidetes. The phyla Proteobacteria and Firmicutes were dominant in all antibiotic containing water samples, with the clones belonged to Deltaproteobacteria and Epsilonproteobacteria significantly abundant, as well as Gram-positive low GC bacteria in the classes Clostridia and Bacilli. It thus seemed that Deltaproteobacteria, Epsilonproteobacteria, Clostridia and Bacilli might be specifically associated with antibiotic containing environments.

Superiority of D-zone Testing Method over Standard Method to detect Rnducible Resistance in Gram Positive Bacteria: a Prospective Surveillance from a Teaching Hospital in Saudi Arabia

OBJECTIVE

In this prospective study, we determined phenotypic resistance to erythromycin among gram positive bacteria.

METHODS

BACTERIAL ISOLATES WERE IDENTIFIED BY CONVENTIONAL METHODS AND BY THE MICROSCAN: D-test zone was performed according to the Clinical and Laboratory Standards institutes (CLSI) recommendations to determine inducible resistance to clindamycin on gram positive bacteria isolated from different clinical specimens. Bacterial isolates included : group A streptococci (GAS), group B streptococci (GBS), viridans streptococci, S.pneumoniae, Staphylococcus aureus (S.aureus) (both methicillin susceptible (MSSA) and methicillin resistant (MRSA).

RESULTS

A total of 1072 gram positive bacterial isolates were tested. The majority was from swabs collected from outpatient clinics. Erythromycin resistance was 8/23 (35%) for S. pneumoniae, 12/91(13%) for GAS and 17/300(5.7%) for GBS. All GAS and viridans streptococci possessed the efflux phenotype only, 8(8.8% and 1(20%), respectively. For GBS, cMLS(B) was 11(3.7%), 3 (1%) iMLS(B) and 2(0.33%) were of efflux phenotype. All S.pneumoniae strains possessed cMLS(B) phenotype. Seventy five isolates (16.3%) of MSSA were resistant to erythromycin compared to 160(83%) of MRSA. The majority of MSSA, 31/460 (6.7%) had an efflux phenotype while 26/460(5.6%) were of cMLS(B) and 19/460(4%) iMLS(B) phenotypes. Constitutive MLS(B) was the most predominant resistant phenotype, 152/193(78.8%) among MRSA.

CONCLUSION

D-test zone should be considered for routine testing to detect inducible clindamycin resistance among significant gram positive bacteria.

PCR-RFLP assay for species and subspecies differentiation of the Streptococcus bovis group based on groESL sequences

The sequence diversity of groESL genes among Streptococcus bovis group isolates was analysed, including five reference strains and 36 clinical isolates. Phylogenetic analysis of the groES and groEL sequences showed that the isolates that belonged to the same species or subspecies usually clustered together. The intergenic spacer region between groES and groEL was variable in size (67–342 bp) and sequence and appeared to be a unique marker for species or subspecies determination. Sequence similarities of the groESL genes among species and subspecies ranged from 84.2 to 99.0 % in groES, and from 88.0 to 99.0 % in groEL. Based on the sequences determined, a Streptococcus bovis group-specific PCR assay was developed, which may provide an alternative means of distinguishing the bovis group from other viridans streptococci. Restriction digestion of the amplicon with AclI further differentiated the species and subspecies.

Prevalence of the erm(T) gene in clinical isolates of erythromycin-resistant group D Streptococcus and Enterococcus

Among 48 erythromycin-resistant group D streptococci (GDS), 36 had the erm(T) resistance gene. erm(T) was also found in 4 of 31 erythromycin-resistant Enterococcus faecium isolates. This is the first report of the erm(T) gene in U.S. GDS isolates and the first report of the erm(T) gene in enterococci.

Characteristics of Streptococcus bovis endocarditis and its differences with Streptococcus viridans endocarditis

The purpose of this study was to evaluate the characteristics of infective endocarditis (IE) caused by S. bovis and compare them to those caused by streptococci of the viridans group (SVG). A prospective study was undertaken considering 55 consecutive cases of IE due to S. bovis and 41 to SVG over 18 years. The study was divided into two periods (1988-1996 and 1997-2005). S. bovis caused 24% of the IE in our centre and constituted the main aetiology for this disease, showing an increase of 358% during the second period studied. Biotype I was responsible for 94.5% of cases and there was a high degree of association with colon tumours (53%). Over the period of the study, 107 patients admitted to our hospital had bacteraemia caused by S. bovis and 310 patients had bacteraemia caused by SVG. In the first group, 55 (51%) were endocarditis cases, but only 41 (13%) of the patients with SVG bacteraemia had endocarditis (p < 0.0001). The distinguishing features of endocarditis caused by S. bovis in comparison with those caused by SGV were: a greater increase in cases during the 2nd period studied (from 12 to 43 vs. from 19 to 22, p < 0.01), a higher percentage of males (93% vs. 71%, p < 0.004), patients significantly older (median age 66 vs. 58.5, p < 0.004), less predisposing cardiopathy (42% vs. 76%, p < 0.0009), more bivalvular involvement (42% vs. 22%, p < 0.04), more spondylitis (9% vs. 0%, p < 0.04), a higher association with colonic tumours (53% vs. 5%, p < 0.0001), and a higher percentage of antibiotic resistance: erythromycin 66% vs. 19%, p < 0.0001; clindamycin 67% vs. 11%, p < 0.0001; cotrimoxazole 77% vs. 30.5%, p < 0.0001, respectively. IE due to S. bovis is an emergent disease in our environment, presenting different characteristics to those produced by SVG.

Development and application of real-time PCR assays for quantification of erm genes conferring resistance to macrolides-lincosamides-streptogramin B in livestock manure and manure management systems

Erythromycin and tylosin are commonly used in animal production, and such use is perceived to contribute to the overall antimicrobial resistance (AR) reservoirs. Quantitative measurements of this type of AR reservoir in microbial communities are required to understand AR ecology (e.g., emergence, persistence, and dissemination). We report here the development, validation, and use of six real-time PCR assays for quantifying six classes of erm genes (classes A through C, F, T, and X) that encode the major mechanism of resistance to macrolides-lincosamides-streptogramin B (MLS(B)). These real-time PCR assays were validated and used in quantifying the six erm classes in five types of samples, including those from bovine manure, swine manure, compost of swine manure, swine waste lagoons, and an Ekokan upflow biofilter system treating hog house effluents. The bovine manure samples were found to contain much smaller reservoirs of each of the six erm classes than the swine manure samples. Compared to the swine manure samples, the composted swine manure samples had substantially reduced erm gene abundances (by up to 7.3 logs), whereas the lagoon or the biofilter samples had similar erm gene abundances. These preliminary results suggest that the methods of manure storage and treatment probably have a substantial impact on the persistence and decline of MLS(B) resistance originating from food animals, thus likely affecting the dissemination of such resistance genes into the environment. The abundances of these erm genes appeared to be positively correlated with those of the tet genes determined previously among these samples. These real-time PCR assays provide a rapid, quantitative, and cultivation-independent measurement of six major classes of erm genes, which should be useful for ecological studies of AR.

High-level gentamicin resistance mediated by a Tn4001-like transposon in seven nonclonal hospital isolates of Streptococcus pasteurianus

We report on the first occurrence of high-level gentamicin resistance (MICs > or = 512 microg/ml) in seven clinical isolates of Streptococcus pasteurianus from Hong Kong. These seven isolates were confirmed to be the species S. pasteurianus on the basis of nucleotide sequencing of the superoxide dismutase (sodA) gene. Epidemiological data as well as the results of pulse-field gel electrophoresis analysis suggested that the seven S. pasteurianus isolates did not belong to the same clone. Molecular characterization showed that they carried a chromosomal, transposon-borne resistance gene [aac(6')Ie-aph(2'')Ia] which was known to encode a bifunctional aminoglycoside-modifying enzyme. The genetic arrangement of this transposon was similar to that of Tn4001, a transposon previously recovered from Staphylococcus aureus and other gram-positive isolates. Genetic linkage with other resistance elements, such as the ermB gene for erythromycin resistance, was not evident. On the basis of these findings, we suggest that routine screening for high-level gentamicin resistance should be recommended for all clinically significant blood culture isolates. This is to avoid the inadvertent use of short-course combination therapy with penicillin and gentamicin, which may lead to the failure of treatment for endocarditis, the selection of drug-resistant Streptococcus pasteurianus and other gram-positive organisms, as well as the unnecessary usage of gentamicin, a drug with potential toxicity.

Identification of an erm(T) gene in strains of inducibly clindamycin-resistant group B Streptococcus

Five inducibly clindamycin (CLI)-resistant group B Streptococcus (GBS) isolates, all negative for erm(A) and erm(B) genes, were found to contain erm(T), a gene previously reported in erythromycin-resistant animal isolates of Lactobacillus spp. and human isolates of Streptococcus bovis. One additional GBS isolate, constitutively resistant to CLI, was also positive for the erm(T) gene in addition to erm(B). To our knowledge, this is the 1st report of erm(T) in GBS, the 2nd bacterial species from humans in which the erm(T) gene has been identified, and the 3rd erm gene to be found in GBS.

The erm(T) gene is flanked by IS1216V in inducible erythromycin-resistant Streptococcus gallolyticus subsp. pasteurianus

We investigated the sequence and the genetic context of the erm(T) gene in six inducible erythromycin-resistant Streptococcus gallolyticus subsp. pasteurianus (formerly S. bovis biotype II.2) isolates. In all isolates, the erm(T) genes were flanked by two IS1216V-like elements with the same polarity and were found to be inserted in the chromosome.

Molecular epidemiology of Streptococcus bovis causing endocarditis and bacteraemia in Italian patients

Streptococcus bovis is being recognised increasingly as a cause of infective endocarditis, and has also been associated with underlying gastrointestinal malignancy. This study evaluated the molecular epidemiology of S. bovis isolates responsible for endocarditis or bacteraemia in Italian patients between January 1990 and August 2003. S. bovis isolates were classified on the basis of their biochemical profiles, antimicrobial susceptibilities and genotypes. Of 25 isolates studied, 20 were S. bovis I and five were S. bovis II. Seven biochemical profiles were identified. Pulsed-field gel electrophoresis (PFGE) analysis identified 22 profiles that differed by at least two DNA fragments and showed a similarity of < 87%. Most PFGE patterns represented single isolates that differed in antimicrobial susceptibility, but three PFGE types were observed, with identical profiles and antibiotypes, in isolates from two different patients. S. bovis I and II isolates grouped into two distinct genetic clusters (I and II) with a similarity coefficient of 38%. Two sub-clusters (Ia and Ib), with a similarity coefficient of 47%, included 17 S. bovis I isolates with similar biochemical profiles (15 with biotype A, and two with biotype B), but different resistance phenotypes. Based on the phenotypic and genotypic heterogeneity of the isolates, it is postulated that the increase in S. bovis endocarditis in this geographical area might have been caused by the selection of sporadic endemic clones from the endogenous intestinal flora.

Genetic basis of antibiotic resistance in clinical isolates of Streptococcus gallolyticus (Streptococcus bovis)

Among 128 Streptococcus gallolyticus (Streptococcus bovis) isolates, 77.7% were resistant to tetracyclines and contained tet(M) and/or tet(L) and/or tet(O). A total of 59.4% had macrolide resistance and contained erm(B) and, rarely, mef(A). Among the one-third of isolates highly resistant to kanamycin and streptomycin, most harbored aphA3 and aad-6 genes.

In vitro activity of telithromycin against viridans group streptococci and Streptococcus bovis isolated from blood: antimicrobial susceptibility patterns in different groups of species

The in vitro activities of penicillin, erythromycin, clindamycin, and telithromycin were determined against 155 viridans group streptococci (VGS) and 18 Streptococcus bovis blood isolates. Heterogeneity in the susceptibility patterns and macrolide resistance phenotypes and genotypes in the different groups of VGS was detected. We found seven telithromycin-resistant S. bovis isolates all harboring the erm(B) gene.

Polyclonal Spread of Erythromycin-ResistantStreptococcus agalactiaein Southern Taiwan

Resistance to erythromycin is common among Streptococcus agalactiae in Taiwan, however the genetic relatedness of erythromycin-resistant isolates has not yet been reported. From 1991 to 2001, 629 clinical isolates of S. agalactiae were collected in a medical center at Tainan in southern Taiwan, of which 189 (30.0%) were resistant to erythromycin. The isolation rate of erythromycin-resistant group B streptococcus (GBS) was stable, irrespective of the clinical sources or study period. Among them, 145 (76.7%) isolates showed the macrolide-lincosamide-streptogramin B (MLS)-resistant phenotype, and 44 (23.3%) had the macrolide (M)- resistant phenotype. Of the isolates with MLS phenotype, 141 (97.2%) isolates harbored the ermB gene alone and only three (2.1%) the ermTR gene, whereas 41 (93.2%) of 44 isolates with M phenotype harbored the mefA/E gene. Of 177 typeable isolates, there were 26 unrelated pulsed-field gel electrophoresis (PFGE) patterns. PFGE type 1 accounted for 17.8% (24/135) of MLS phenotype isolates with the ermB gene and 48.7% (18/37) of M phenotype isolates with the mefA/E gene. During the study period, the proportion of PFGE type 6 decreased significantly, whereas that of type 8 increased. Our results suggest that erythromycin resistance is not uncommon among clinical isolates of S. agalactiae and is, at least, partially related to polyclonal spread in southern Taiwan.

Phenotypic and molecular characterization of erythromycin resistance in four isolates of Streptococcus-like gram-positive cocci causing bacteremia

Among nine patients with bacteremia caused by Granulicatella or Gemella in a 6-year period (July 1995 to June 2001), three had bacteremia caused by erythromycin-resistant Granulicatella adiacens and one had bacteremia caused by erythromycin-resistant Gemella haemolysans. All four isolates possessed mef genes, whereas none possessed ermT, ermTR, or ermB genes.

Phenotypic and genetic characterization of resistance against macrolides and lincosamides in Streptococcus gallolyticus strains isolated from pigeons and humans

The macrolide and lincosamide (ML) resistance phenotype of 65 pigeon and 30 human Streptococcus gallolyticus strains was determined by the disk diffusion method. Constitutive resistance against the tested antibiotics was seen in 13 human and 28 pigeon strains. Simultaneous screening for the presence of erm(B) and mef(A) genes using PCR revealed that the erm(B) gene was present in 40 out of these 41 phenotypically resistant S. gallolyticus strains while the mef(A) gene was detected in only one resistant and one susceptible human-derived strain. The erm(B) genes of 10 human and 10 pigeon S. gallolyticus strains were sequenced and compared. Four human and seven pigeon strains possessed exactly the same sequence for the erm(B) gene. The sequence of the erm(B) gene of the remaining strains differed in one to five nucleotides. These findings could indicate a possible exchange of resistance genes between human and pigeon strains.

Clinical and molecular epidemiology of erythromycin-resistant beta-hemolytic lancefield group G streptococci causing bacteremia

Among 100 patients with group G beta-hemolytic streptococcal bacteremia in a 6-year period (1997 to 2002), seven had bacteremia caused by erythromycin-resistant strains. Five of the seven patients had cellulitis and/or abscesses. The two isolates resistant to erythromycin and clindamycin possessed erm genes, one ermTR and the other ermB. The five isolates resistant to erythromycin but sensitive to clindamycin and one of those resistant to both erythromycin and clindamycin possessed mef genes.

Geographical difference of disease association in Streptococcus bovis bacteraemia

From 1996 to 2001, 48 Streptococcus bovis strains were isolated from blood cultures of 37 patients in one hospital. Median patient age was 68 years (range: 1 day-88 years). The male : female ratio was 23 : 14. Most patients (97 %) had underlying diseases, including biliary tract disease in 14 (38 %), diabetes mellitus in 12 (32 %), liver parenchymal disease in seven (19 %), carcinoma of the colon in four (11 %) and other malignancies in four (11 %). No infective foci (indicative of primary bacteraemia) were identified in 15 patients (40 %) and 14 (38 %) had acute cholangitis/cholecystitis, but only four (11 %) had infective endocarditis. Two (5 %), three (8 %) and 32 (87 %) patients had S. bovis of biotypes I, II/1 and II/2, respectively, and three (8 %), two (5 %) and 32 (87 %) patients had S. bovis of genotypes 1, 2a and 2b, respectively. All isolates were sensitive to penicillin, cephalothin and vancomycin, 24 (65 %) were resistant to erythromycin and 15 (41 %) were resistant to clindamycin (these strains were also resistant to erythromycin). Thirteen isolates that were erythromycin- and clindamycin-resistant possessed the ermB gene, 10 possessed the ermT gene and one possessed both the ermB and ermT genes. Overall, seven patients (19 %) died. In contrast to most other reports from western countries, where carcinoma of the colon and infective endocarditis were the major underlying disease and infective focus associated with S. bovis bacteraemia, biliary tract disease and acute cholangitis and/or cholecystitis were the major underlying diseases associated with S. bovis bacteraemia in our locality.

Distribution of tetracycline resistance genes tet(M), tet(O), tet(L) and tet(K) in blood isolates of viridans group streptococci harbouring erm(B) and mef(A) genes. Susceptibility to quinupristin/dalfopristin and linezolid

Susceptibility to erythromycin, tetracycline, clindamycin, quinupristin/dalfopristin and linezolid was investigated using 111 consecutive non-duplicate blood culture isolates of viridans-group streptococci (VGS). The erm(B) and mef(A) genes were detected, either alone or in combination, in the 47 (42%) erythromycin-resistant strains. The tet(M) gene alone was predominant (78%) in the 36 (35%) tetracycline-resistant isolates. Two isolates carried the tet(O) gene alone and two others the tet(L) associated with tet(O) or tet(M). The association between erythromycin and tetracycline resistance was common and the erm(B) and tet(M) determinants seem to be associated in our VGS. We found three isolates resistant to quinupristin/dalfopristin, all of them were erythromycin and tetracycline-resistant. For all isolates tested, linezolid MICs were <or=2 mg/l.

Streptococcus bovis revisited: a clinical review of 81 bacteremic episodes paying special attention to emerging antibiotic resistance

Following 2 Cases of Streprococcus bovis endocarditis with a high level of resistance to clindamycin during 2002, the authors reviewed their clinical experience with S. bovis bacteremia during 2 periods, starting in 1980. 81 episodes of S. bovis bacteremia represented approximately 1% of all episodes of bacteremia. In 32 (40%) cases the bacteremia represented endocarditis, in 15 (19%) the bacteremia originated from sick bowel, 11 (14%) were suspected to arise from urinary tract infection, 10 (12%) originated from biliary or peritoneal infection, and 13 from other or unknown sources. 25 (31%) of the bacteremias were polymicrobial. All of the isolates were highly susceptible to penicillin and clindamycin, with the following exceptions: 2 isolates had a minimal inhibitory concentration (MIC) of 0.5 mg/l to penicillin (in 1997) and 5 isolates had an MIC of > 2 mg/l to clindamycin (in 1997, 1998, 2000 and 2002). The 2 most recent of these 5 had high-level resistance to clindamycin of > 256 mg/l. It seems that clindamycin resistance in S. bovis is an emerging phenomenon, in contrast to penicillin resistance, high levels of which have not yet been described in S. bovis.