Presence of plasmid pA15 correlates with prevalence of constitutive MLS(B) resistance in group A streptococcal isolates at a university hospital in southern Taiwan

A systematic review of antibiotics and antibiotic resistance genes (ARGs) in mariculture wastewater: Antibiotics removal by microalgal-bacterial symbiotic system (MBSS), ARGs characterization on the metagenomic

Antibiotic residues in mariculture wastewater seriously affect the aquatic environment. Antibiotic Resistance Genes (ARGs) produced under antibiotic stress flow through the environment and eventually enter the human body, seriously affecting human health. Microalgal-bacterial symbiotic system (MBSS) can remove antibiotics from mariculture and reduce the flow of ARGs into the environment. This review encapsulates the present scenario of mariculture wastewater, the removal mechanism of MBSS for antibiotics, and the biomolecular information under metagenomic assay. When confronted with antibiotics, there was a notable augmentation in the extracellular polymeric substances (EPS) content within MBSS, along with a concurrent elevation in the proportion of protein (PN) constituents within the EPS, which limits the entry of antibiotics into the cellular interior. Quorum sensing stimulates the microorganisms to produce biological responses (DNA synthesis - for adhesion) through signaling. Oxidative stress promotes gene expression (coupling, conjugation) to enhance horizontal gene transfer (HGT) in MBSS. The microbial community under metagenomic detection is dominated by aerobic bacteria in the bacterial-microalgal system. Compared to aerobic bacteria, anaerobic bacteria had the significant advantage of decreasing the distribution of ARGs. Overall, MBSS exhibits remarkable efficacy in mitigating the challenges posed by antibiotics and resistant genes from mariculture wastewater.

Persistent versus transient, and conventional plastic versus biodegradable plastic? -Two key questions about microplastic-water exchange of antibiotic resistance genes

The ubiquitous microplastics (MPs) in water environment play an important role in the dissemination of antibiotic resistance genes (ARGs) due to their exchange between floating MPs and receiving waters. However, whether the ARG exchange is persistent or transient and what are the differences in ARG exchange between conventional plastics and biodegradable plastics are the two key issues to be addressed. In this study, biodegradable PBAT and non-biodegradable PET MPs were chosen to explore the MP-water ARG exchange after the MPs floated to the receiving waters. The results demonstrated that the active exchange of ARGs between MPs and receiving waters occurred, which, however, were transient for most of ARGs. The relative abundance of ARGs both on the MPs and in the waters rapidly decreased to the initial or lower levels within 4 weeks. Approximately 25-50% (ARG subtype number ratio) of studied ARG subtypes were introduced into the receiving waters by MPs, and 35-65% of studied ARG subtypes went through fluctuation in terms of abundance on MPs and in the receiving water. ARGs tended to converge between MPs and the receiving waters with time. Furthermore, the ARG exchange between MPs and waters facilitated horizontal gene transfer (HGT). IntI1 and tnpA05 played the crucial roles in HGT, which was indicated by their correlated change with most ARGs; in contrast, tnpA04 showed the obvious lagging responses. The biodegradable MP of PBAT generally accumulated higher levels of most ARGs including multidrug resistant genes than the non-biodegradable MP of PET. The transient exchange of most ARGs between MPs and water implies that the on-off hitchhiking of ARGs on MPs in aquatic environment may not exert significant influence on ARG transmission. However, compared with the conventional plastics, the biodegradable MPs might pose much higher ARG dissemination risks due to the higher enrichment of ARGs particularly with people's ever-increasingly usage. Enough attention must be paid to this emerging issue.

β-Lactam Resistance Gene NDM-1 in the Aquatic Environment: A Review

New Delhi Metallo-β-lactamase-1 (NDM-1) offers carbapenem antibiotics resistance that creates an evolving challenge in treating bacterial infections. NDM-1-bearing strains were observed in surface waters around New Delhi in 2010 and after then identified globally. The usage of antibiotics may hasten the growth of the NDM-1-producing bacteria, which pose severe hazards to human and animal health. The emergence of the NDM-1 in the aquatic environment is turning out to be a growing concern worldwide. NDM-1 gene conferring resistance to a widespread class of antibiotics has been observed in bacteria disseminated in animal production wastewaters, hospital sewage, domestic sewage, industrial effluents, wastewater treatment plants, drinking water, surface water, and even in groundwater. This review recapitulates the currently published research studies on the prevalence and geographical distribution of the NDM-1 gene in the aquatic environment, its habitats, and healthcare risk associated with NDM-1-producing bacteria, in addition to molecular techniques employed to reveal the occurrence of the NDM-1 in the aquatic environment, including conventional polymerase chain reaction, real-time qPCR, DNA hybridization, and microarray-based methods.

Global genomic epidemiology of Streptococcus pyogenes

Streptococcus pyogenes is one of the Top 10 human infectious disease killers worldwide causing a range of clinical manifestations in humans. Colonizing a range of ecological niches within its sole host, the human, is key to the ability of this opportunistic pathogen to cause direct and post-infectious manifestations. The expansion of genome sequencing capabilities and data availability over the last decade has led to an improved understanding of the evolutionary dynamics of this pathogen within a global framework where epidemiological relationships and evolutionary mechanisms may not be universal. This review uses the recent publication by Davies et al., 2019 as an updated global framework to address S. pyogenes population genomics, highlighting how genomics is being used to gain new insights into evolutionary processes, transmission pathways, and vaccine design.

Selectively enrichment of antibiotics and ARGs by microplastics in river, estuary and marine waters

The partition of antibiotics and antibiotic resistant genes (ARGs) between the microplastics (MPs) and the surrounding water with various salinity are still unclear. In this study, we hypothesized that adsorption of antibiotics on MPs might cause a significant change of the structure of microbial communities, diversity and abundance of ARGs on MPs and this might be further affected by change of salinity. In this study, we investigated adsorption of four common antibiotics (sulfamerazine, tetracycline, chloramphenicol and tylosin) to polyethylene (PE) MPs in river, estuary and marine waters, and the differences of antibiotic resistant genes (ARGs) and bacterial communities on MPs and in the three waters. The results showed that MPs can enrich antibiotics, ARGs and microbes from the surrounding water. Elevated salinity could reduce adsorption of antibiotics to MPs and the abundance of ARGs. For example, MPs can concentrate more antibiotics and ARGs in the fresh river water than in the estuary and the marine waters. In addition, ARGs and bacterial communities on MPs at various salinity were significantly different under the pressure of four antibiotics. On MPs, sul1, sulA/folP-01, tetA, tetC, tetX and ermE increased significantly but a few new ARGs such as sulA/folP-01 and tetA appeared. The structure of the bacterial communities on MPs was different from the surrounding water since some bacteria species found on MPs were barely detected in the surrounding water while some genera on MPs vanished after exposure to antibiotics. As the antibiotics adsorbed and the ARGs on MPs decreased with the water salinity, the structure of the communities on MPs thus varied with salinity change. These findings are important to understand the effects of MPs on the transport, fate and ecological risk of antibiotics and ARGs in different aquatic environments.

Distribution of Antibiotic Resistance Genes in Three Different Natural Water Bodies-A Lake, River and Sea

Currently, due to abuse in the use of human antibiotics and the weak regulatory control that the authorities have over sewage discharge and manure management, antibiotic resistance genes (ARGs) have become a new type of environmental pollutant. Three different natural water bodies (Poyang Lake, Haihe River and Qingdao No.1 Bathing Beach seawater) were sampled during the same periods to conduct a longitudinal comparison of distribution. The distribution and expression of 11 ARGs in 20 species were studied, and the correlations between the expression and the distribution of time and space of the ARGs in different water bodies were also analyzed. With the exception of ermA, blaNDM-1 and vanA, which were not detected in seawater, the other ARGs could be detected in all three water bodies. Tetracycline resistance genes (tetC, tetM and tetQ) in the seawater and Haihe River had even reached 100%, and sulfa ARGs (sul1 and sul2) in the seawater and Poyang Lake, as well as sul2 and sul3 in the Haihe River, had also reached 100%. The ARG pollution in Haihe River was much more serious, since 14 and 17 of 20 ARG species were significantly higher compared with seawater and Poyang Lake, respectively. Some ARGs also had a high absolute abundance. The absolute abundance of macrolide resistance genes (ermB) in seawater was as high as 8.61 × 10⁷ copies/L, and the anti-tuberculosis resistant genes (rpoB and katG) in the Haihe River Basin were highly abundant at 1.32 × 10⁶ copies/L and 1.06 × 10⁷ copies/L, respectively. This indicates that ARGs have gradually become more diverse and extensive in natural water bodies. The results of a redundancy analysis (RDA) of the three water bodies showed that although each water body is affected by different factors in space and time, overall, the presence of AGRs is closely related to the production and life of human beings and the migration of animals.

Highly prevalent emmSTG840.0 and emmSTC839.0 types of erythromycin non-susceptible group G Streptococcus isolated from bacteremia in southern Taiwan

BACKGROUND/PURPOSE

Group G Streptococcus (GGS) infections in human have increased. Treatment relied on antibiotic therapy, including erythromycin. However, information regarding the dominant strains and erythromycin susceptibility in GGS bacteremia is limited.

METHODS

A total of 134 GGS were isolated from patients with bacteremia in a university hospital of southern Taiwan during 1993-2010. The erythromycin susceptibility was determined by disc diffusion and agar dilution assays. The bacterial species was determined by MALDI-TOF. The presence of erythromycin-resistant genes and emm types were determined by polymerase chain reaction and sequence. The clonal spreading was analyzed by pulsed-field gel electrophoresis with SmaI or SgrAI digestion.

RESULTS

The annual erythromycin non-susceptible rate varied, with an average of 40.3%. All erythromycin non-susceptible strains belonged to the Streptococcus dysgalactiae. No erythromycin non-susceptible strains belong to the anginosus group. The most prevalent erythromycin-resistant gene was mefA (57.4%), followed by ermB (37%), and ermA (3.7%). The N terminal hyper variable region of emm was sequenced to determine the emm type, and only S. dysgalactiae had the emm gene. The most prevalent emm types were emmSTG840.0 (17.2%), emmSTG485.0 (10.4%), and emmSTC839.0 (9.0%). 73% and 47% of the strains with only mefA and ermB belonged to emmSTG840.0 and emmSTC839.0 types, respectively. Pulsed-field gel electrophoresis showed that different clones of emmSTG840.0 and emmSTC839.0 strains were spread in this region during the 18 years of surveillance.

CONCLUSION

Our data indicate that there were dominant emm types with erythromycin non-susceptibility in S. dysgalactiae isolated from bacteremia in Taiwan, and thus constant surveillance is warranted.

Presence and distribution of Macrolides-Lincosamide-Streptogramin resistance genes and potential indicator ARGs in the university ponds in Guangzhou, China

This study aimed to determine the occurrence, abundance, and variation of seven Macrolides-Lincosamide-Streptogramin (MLS) resistance genes (ereB, ermA, ermB, ermF, mefA, vatB, mphA) and six potential indicator ARGs (tet (B), sul1, qnrS, fexA, IntI1, ermB) from three ponds at university by quantitative PCR and assess the impacts on the surroundings. Solid samples (fish feces, soil and sediment) and water samples were tested. All the genes were found at low levels in soil samples. For the MLS resistance genes, only two MLS genes (ermB, ermF) were detected in all samples and significant correlations between ermB and Σ MLS (R = 0.91 in solid samples; R = 0.86 in water samples, p < 0.01) were found. For the potential indicators, intl1 and sul1 were present at high levels in the three different ponds while the other genes showed varying levels. These findings show that the ermB gene can probably be served as an indicator to evaluate the overall level of MLS resistance genes. The fairly low abundance of all the tested resistance genes in soil samples and the moderate levels in other samples suggests that the university ponds kept a good state and did not have a significant impact on their surroundings.

Genomics of high molecular weight plasmids isolated from an on-farm biopurification system

The use of biopurification systems (BPS) constitutes an efficient strategy to eliminate pesticides from polluted wastewaters from farm activities. BPS environments contain a high microbial density and diversity facilitating the exchange of information among bacteria, mediated by mobile genetic elements (MGEs), which play a key role in bacterial adaptation and evolution in such environments. Here we sequenced and characterized high-molecular-weight plasmids from a bacterial collection of an on-farm BPS. The high-throughput-sequencing of the plasmid pool yielded a total of several Mb sequence information. Assembly of the sequence data resulted in six complete replicons. Using in silico analyses we identified plasmid replication genes whose encoding proteins represent 13 different Pfam families, as well as proteins involved in plasmid conjugation, indicating a large diversity of plasmid replicons and suggesting the occurrence of horizontal gene transfer (HGT) events within the habitat analyzed. In addition, genes conferring resistance to 10 classes of antimicrobial compounds and those encoding enzymes potentially involved in pesticide and aromatic hydrocarbon degradation were found. Global analysis of the plasmid pool suggest that the analyzed BPS represents a key environment for further studies addressing the dissemination of MGEs carrying catabolic genes and pathway assembly regarding degradation capabilities.

Omega (ParB) binding sites together with the RNA polymerase-recognized sequence are essential for centromeric functions of the Pωregion in the partition system of pSM19035

Partition systems contribute to stable plasmid inheritance in bacteria through the active separation of DNA molecules to daughter cells, and the centromeric sequence located either upstream or downstream of canonical partition operons plays an important role in this process. A specific DNA-binding protein binds to this sequence and interacts with the motor NTPase protein to form a nucleoprotein complex. The inc18-family plasmid pSM19035 is partitioned by products of δ and ω genes, with δ encoding a Walker-type ATPase and ω encoding a DNA-binding protein. As the two genes are transcribed separately, this system differs from others in its organization; nonetheless, expression of these genes is regulated by Omega, which also regulates the copy number of the plasmid (by controlling copS gene expression). Protein Omega specifically recognizes WATCACW heptad repeats. In this study, we constructed a synthetic δω operon to enable an analysis of the centromeric functions of Omega-binding sites Pδ, Pω and PcopS, discrete from their promoter functions. Our results show that these three regions do not support plasmid stabilization equally. We demonstrate that the Pω site alone can simultaneously drive the expression of partition genes from the synthetic δω operon and act as a unique centromeric sequence to promote the most efficient plasmid partitioning. Moreover, Pω can support the centromeric function in concert with the synthetic δω operon expressed from a heterologous promoter demonstrating that Pω is the main centromeric sequence of the δ-ω partition system. Additionally, the RNA polymerase-recognized sequence in Pω is essential for its centromeric function.

Small plasmids in Streptococcus dysgalactiae subsp. equisimilis isolated from human infections in southern India and sequence analysis of two novel plasmids

Small plasmids are frequently found in S. pyogenes isolates from human infections in India. Streptococcus dysgalactiae subsp. equisimilis (SDSE) is a streptococcal subspecies that is genetically similar to S. pyogenes and has a similar ecology. Therefore, we determined the distribution of small plasmids in a collection of 254 SDSE isolates, comprising 44 different emm-types and emm non-typable strains, from southern India, utilizing an established PCR based method. Briefly, 1.2% (n=3) of the isolates were positive for repA (encoding the replication initiation protein A) and 1.6% (n=4) were repB positive (encoding the replication initiation protein B). One isolate (G315) showed a co-detection of repB and dysA (encoding the bacteriocin dysgalacticin) which is characteristic for previously described pDN281/pW2580-like plasmids, observed in SDSE and S. pyogenes. The remaining plasmid bearing isolates showed no characteristic co-detection of known plasmid-associated genes. Thus, plasmids pG271 and pG279, representatives for repB and repA harboring plasmids, respectively, were analyzed. The plasmids pG271 and pG279 could be assigned to the pMV158 and the pC194/pUB110 family of rolling-circle plasmids, respectively. Like the characterized small native plasmids of S. pyogenes from India, the SDSE plasmids discovered and described in this study did not carry any of the known antibiotic resistance genes. SDSE bore less of the investigated small native plasmids that were distinct from the small native plasmids of S. pyogenes of the same geographic region. This indicates a low rate of lateral transfer of these genetic elements between these two related streptococcal species.

Distribution of small native plasmids in Streptococcus pyogenes in India

Complete characterization of a Streptococcus pyogenes population from a defined geographic region comprises information on the plasmids that circulate in these bacteria. Therefore, we determined the distribution of small plasmids (<5kb) in a collection of 279 S. pyogenes isolates from India, where diversity of strains and incidence rates of S. pyogenes infections are high. The collection comprised 77 emm-types. For plasmid detection and discrimination, we developed PCRs for different plasmid replication initiation protein genes, the putative repressor gene copG and bacteriocin genes dysA and scnM57. Plasmid distribution was limited to 13 emm-types. Co-detection analysis using aforementioned PCRs revealed four distinct plasmid sub-types, two of which were previously unknown. Representative plasmids pA852 and pA996 of the two uncharacterized plasmid sub-types were sequenced. These two plasmids could be assigned to the pMV158 and the pC194/pUB110 family of rolling-circle plasmids, respectively. The majority of small plasmids found in India belonged to the two newly characterized sub-types, with pA852- and pA996-like plasmids amounting to 42% and 22% of all detected plasmids, respectively. None of the detected plasmids coded for a known antibiotic resistance gene. Instead, all of the four plasmid sub-types carried known or potential bacteriocin genes. These genes may have influence on the evolutionary success of certain S. pyogenes genotypes. Notably, pA852-like plasmids were found in all isolates of the most prevalent emm-type 11.0. Together, a priori fitness of this genotype and increased fitness due to the acquired plasmids may have rendered type emm11.0 successful and caused the prevalence of pA852-like plasmids in India.

Arrangement and number of clustered regularly interspaced short palindromic repeat spacers are associated with erythromycin susceptibility in emm12, emm75 and emm92 of group A streptococcus

Clustered regularly interspaced short palindromic repeats (CRISPR) are composed of numerous repeat-spacer units and are considered a prokaryotic defence system against foreign nucleic acids. Since antibiotic-resistant genes are frequently encoded in foreign nucleic acids, the aim of this study was to test whether erythromycin susceptibility in group A streptococcus (Streptococcus pyogenes) is associated with characteristics of CRISPR elements. Erythromycin susceptibility of 330 isolates collected between 1997 and 2003 was analysed. Among 29 emm types, emm12, emm75 and emm92 showed significant changes in erythromycin-resistance rates. By sequencing the spacers from two CRISPR loci, spacer contents in emm12, emm75 and emm92 strains were associated with erythromycin susceptibility. Strains with fewer spacers were more resistant to erythromycin. Moreover, in emm4 strains, which showed no significant change in their annual erythromycin-resistance rate, CRISPR type and number of spacers were not correlated with erythromycin susceptibility. These results highlight a novel association between CRISPR spacer content and erythromycin susceptibility in group A streptococcus.

Prevalence of clinically relevant antibiotic resistance genes in surface water samples collected from Germany and Australia

The prevalence and proliferation of antibiotic resistant bacteria is profoundly important to human health, but the extent to which aquatic environments contribute toward the dissemination of antibiotic resistant genes (ARGs) is poorly understood. The prevalence of 24 ARGs active against eight antibiotic classes (β-lactams, aminoglycosides, glycopeptides, chloramphenicols, tetracycline, macrolides, trimethoprim, and sulfonamides) was evaluated in surface water samples collected from Germany and Australia with culture independent methods. The ARGs most frequently detected both in Germany and Australia were sulI, sulII (77-100%), and dfrA1 (43-55%) which code for resistance to sulfonamide and trimethoprim. Macrolides resistance gene ermB was relatively more prevalent in the surface water from Germany (68%) than Australia (18%). In contrast, the chloramphenicol resistance gene catII was more frequently detected in Australia (64%) than Germany (9%). Similarly, β-lactams resistance gene ampC was more prevalent in the samples from Australia (36%) than Germany (19%). This study highlights wide distribution of ARGs for sulfonamide, trimethoprim, macroline, β-lactams and chloramphenicol in the aquatic ecosystems. Aquatic ecosystems can therefore be reservoirs of ARGs genes which could potentially be transferred from commensal microorganisms to human pathogens.

Plasmid metagenome reveals high levels of antibiotic resistance genes and mobile genetic elements in activated sludge

The overuse or misuse of antibiotics has accelerated antibiotic resistance, creating a major challenge for the public health in the world. Sewage treatment plants (STPs) are considered as important reservoirs for antibiotic resistance genes (ARGs) and activated sludge characterized with high microbial density and diversity facilitates ARG horizontal gene transfer (HGT) via mobile genetic elements (MGEs). However, little is known regarding the pool of ARGs and MGEs in sludge microbiome. In this study, the transposon aided capture (TRACA) system was employed to isolate novel plasmids from activated sludge of one STP in Hong Kong, China. We also used Illumina Hiseq 2000 high-throughput sequencing and metagenomics analysis to investigate the plasmid metagenome. Two novel plasmids were acquired from the sludge microbiome by using TRACA system and one novel plasmid was identified through metagenomics analysis. Our results revealed high levels of various ARGs as well as MGEs for HGT, including integrons, transposons and plasmids. The application of the TRACA system to isolate novel plasmids from the environmental metagenome, coupled with subsequent high-throughput sequencing and metagenomic analysis, highlighted the prevalence of ARGs and MGEs in microbial community of STPs.

The prevalence of erythromycin resistance in group B streptococcal isolates at a University Hospital in Taiwan

Due to reduced antibiotic consumption in Taiwan, erythromycin resistance rate had decreased in Streptococcus pyogenes, but it increased in Streptococcus pneumoniae. The objectives of the present study were (1) to determine the erythromycin and clindamycin resistance rate and minimum inhibitory concentration (MIC) of the group B streptococcus (GBS) clinical isolates, and (2) to investigate the mechanism responsible for the macrolide, lincosamide, and group B streptogramin (MLS(B)) resistance. A total of 1,395 GBS isolates were collected from June 2001 to April 2007. Forty-four percent of the GBS isolates were resistant to erythromycin, and 39% were resistant to clindamycin. The annual erythromycin resistance rate increased from 32% in 2001 to 51% in 2004; a significant decrease was observed in 2005 (47%), 2006 (42%), and 2007 (38%). Percentage of erythromycin-resistant isolates with erm(B) gene significantly increased from 72% in 2001 to 90% in 2007. We found that the plasmid encoded zeta gene was present in 13% of the resistant isolates, along with erm(B). When compared to our previous study (1991 to May 2001), the overall erythromycin resistance rate increased from 30% to 44%. erm(B) was the major resistant determinant, and zeta toxin encoding plasmid has a limited role in mediating erythromycin resistance unlike in GAS isolates as reported earlier.

Antibiotic resistance genes in water environment

The use of antibiotics may accelerate the development of antibiotic resistance genes (ARGs) and bacteria which shade health risks to humans and animals. The emerging of ARGs in the water environment is becoming an increasing worldwide concern. Hundreds of various ARGs encoding resistance to a broad range of antibiotics have been found in microorganisms distributed not only in hospital wastewaters and animal production wastewaters, but also in sewage, wastewater treatment plants, surface water, groundwater, and even in drinking water. This review summarizes recently published information on the types, distributions, and horizontal transfer of ARGs in various aquatic environments, as well as the molecular methods used to detect environmental ARGs, including specific and multiplex PCR (polymerase chain reaction), real-time PCR, DNA sequencing, and hybridization based techniques.