Integration of pT181-like tetracycline resistance plasmids into large staphylococcal plasmids involves IS257

Staphylococcus haemolyticus: An updated review on nosocomial infections, antimicrobial resistance, virulence, genetic traits, and strategies for combating this emerging opportunistic pathogen

Staphylococcus haemolyticus, a key species of the Staphylococcus genus, holds significant importance in healthcare-associated infections, due to its notable resistance to antimicrobials, like methicillin, and proficient biofilms-forming capabilities. This coagulase-negative bacterium poses a substantial challenge in the battle against nosocomial infections. Recent research has shed light on Staph. haemolyticus genomic plasticity, unveiling genetic elements responsible for antibiotic resistance and their widespread dissemination within the genus. This review presents an updated and comprehensive overview of the clinical significance and prevalence of Staph. haemolyticus, underscores its zoonotic potential and relevance in the one health framework, explores crucial virulence factors, and examines genetics features contributing to its success in causing emergent and challenging infections. Additionally, we scrutinize ongoing studies aimed at controlling spread and alternative approaches for combating it.

The Plasmidomic Landscape of Clinical Methicillin-Resistant Staphylococcus aureus Isolates from Malaysia

Methicillin-resistant Staphylococcus aureus (MRSA) is a priority nosocomial pathogen with plasmids playing a crucial role in its genetic adaptability, particularly in the acquisition and spread of antimicrobial resistance. In this study, the genome sequences of 79 MSRA clinical isolates from Terengganu, Malaysia, (obtained between 2016 and 2020) along with an additional 15 Malaysian MRSA genomes from GenBank were analyzed for their plasmid content. The majority (90%, 85/94) of the Malaysian MRSA isolates harbored 1-4 plasmids each. In total, 189 plasmid sequences were identified ranging in size from 2.3 kb to ca. 58 kb, spanning all seven distinctive plasmid replication initiator (replicase) types. Resistance genes (either to antimicrobials, heavy metals, and/or biocides) were found in 74% (140/189) of these plasmids. Small plasmids (<5 kb) were predominant (63.5%, 120/189) with a RepL replicase plasmid harboring the ermC gene that confers resistance to macrolides, lincosamides, and streptogramin B (MLS_B) identified in 63 MRSA isolates. A low carriage of conjugative plasmids was observed (n = 2), but the majority (64.5%, 122/189) of the non-conjugative plasmids have mobilizable potential. The results obtained enabled us to gain a rare view of the plasmidomic landscape of Malaysian MRSA isolates and reinforces their importance in the evolution of this pathogen.

Presence and characterization of methicillin-resistant Staphylococcus aureus co-carrying the multidrug resistance genes cfr and lsa(E) in retail food in China

Staphylococcus aureus is an important food-related pathogen associated with bacterial poisoning that is difficult to treat due to its multidrug resistance. The cfr and lsa(E) genes both cause multiple drug resistance and have been identified in numerous Staphylococcus species, respectively. In this study, we found that a methicillin-resistant S. aureus (MRSA) strain, 2868B2, which was isolated from a sample of frozen dumplings in Hangzhou in 2015, co-carried these two different multidrug resistance genes. Further analysis showed that this strain was resistant to more than 18 antibiotics and expressed high-level resistance to florfenicol, chloramphenicol, clindamycin, tiamulin, erythromycin, ampicillin, cefepime, ceftazidime, kanamycin, streptomycin, tetracycline, trimethoprim-sulfamethoxazole and linezolid (MIC = 8 μg/mL). Whole genome sequencing was performed to characterize the genetic environment of these resistance genes and other genomic features. The cfr gene was located on the single plasmid p2868B2 (39,159 bp), which demonstrated considerable similarity to many plasmids previously identified in humans and animals. p2868B2 contained the insertion sequence (IS) element IS21-558, which allowed the insertion of cfr into Tn558 and played an important role in the mobility of cfr. Additionally, a novel multidrug resistance region (36.9 kb) harbouring lsa(E) along with nine additional antibiotic resistance genes (ARGs) (aadD, aadE, aacA-aphD, spc, lnu(B), lsa(E), tetL, ermC and blaZ) was identified. The multidrug resistance region harboured four copies of IS257 that were active and can mediate the formation of four circular structures containing ARGs and ISs. In addition, genes encoding various virulence factors and affecting multiple cell adhesion properties were identified in the genome of MRSA 2868B2. This study confirmed that the cfr and lsa(E) genes coexist in one MRSA strain and the presence of plasmid and IS257 in the multi-ARG cluster can promote both ARG transfer and dissemination. Furthermore, the presence of so many ARGs and virulence genes in food-related pathogens may seriously compromise the effectiveness of clinical therapy and threaten public health, its occurrence should pay public attention and the traceability of these genes in food-related samples needs further surveillance.

Mechanisms of Bacterial Resistance to Antimicrobial Agents

During the past decades resistance to virtually all antimicrobial agents has been observed in bacteria of animal origin. This chapter describes in detail the mechanisms so far encountered for the various classes of antimicrobial agents. The main mechanisms include enzymatic inactivation by either disintegration or chemical modification of antimicrobial agents, reduced intracellular accumulation by either decreased influx or increased efflux of antimicrobial agents, and modifications at the cellular target sites (i.e., mutational changes, chemical modification, protection, or even replacement of the target sites). Often several mechanisms interact to enhance bacterial resistance to antimicrobial agents. This is a completely revised version of the corresponding chapter in the book Antimicrobial Resistance in Bacteria of Animal Origin published in 2006. New sections have been added for oxazolidinones, polypeptides, mupirocin, ansamycins, fosfomycin, fusidic acid, and streptomycins, and the chapters for the remaining classes of antimicrobial agents have been completely updated to cover the advances in knowledge gained since 2006.

Plasmid-Mediated Antimicrobial Resistance in Staphylococci and Other Firmicutes

In staphylococci and other Firmicutes, resistance to numerous classes of antimicrobial agents, which are commonly used in human and veterinary medicine, is mediated by genes that are associated with mobile genetic elements. The gene products of some of these antimicrobial resistance genes confer resistance to only specific members of a certain class of antimicrobial agents, whereas others confer resistance to the entire class or even to members of different classes of antimicrobial agents. The resistance mechanisms specified by the resistance genes fall into any of three major categories: active efflux, enzymatic inactivation, and modification/replacement/protection of the target sites of the antimicrobial agents. Among the mobile genetic elements that carry such resistance genes, plasmids play an important role as carriers of primarily plasmid-borne resistance genes, but also as vectors for nonconjugative and conjugative transposons that harbor resistance genes. Plasmids can be exchanged by horizontal gene transfer between members of the same species but also between bacteria belonging to different species and genera. Plasmids are highly flexible elements, and various mechanisms exist by which plasmids can recombine, form cointegrates, or become integrated in part or in toto into the chromosomal DNA or into other plasmids. As such, plasmids play a key role in the dissemination of antimicrobial resistance genes within the gene pool to which staphylococci and other Firmicutes have access. This chapter is intended to provide an overview of the current knowledge of plasmid-mediated antimicrobial resistance in staphylococci and other Firmicutes.

An approach to identifying drug resistance associated mutations in bacterial strains

Background

Drug resistance in bacterial pathogens is an increasing problem, which stimulates research. However, our understanding of drug resistance mechanisms remains incomplete. Fortunately, the fast-growing number of fully sequenced bacterial strains now enables us to develop new methods to identify mutations associated with drug resistance.

Results

We present a new comparative approach to identify genes and mutations that are likely to be associated with drug resistance mechanisms. In order to test the approach, we collected genotype and phenotype data of 100 fully sequenced strains of S. aureus and 10 commonly used drugs. Then, applying the method, we re-discovered the most common genetic determinants of drug resistance and identified some novel putative associations.

Conclusions

Firstly, the collected data may help other researchers to develop and verify similar techniques. Secondly, the proposed method is successful in identifying drug resistance determinants. Thirdly, the in-silico identified genetic mutations, which are putatively involved in drug resistance mechanisms, may increase our understanding of the drug resistance mechanisms.

Identification of a plasmid-borne resistance gene cluster comprising the resistance genes erm(T), dfrK, and tet(L) in a porcine methicillin-resistant Staphylococcus aureus ST398 strain

A novel plasmid-borne resistance gene cluster comprising the genes erm(T) for macrolide-lincosamide-streptogramin B resistance, dfrK for trimethoprim resistance, and tet(L) for tetracycline resistance was identified in a porcine methicillin-resistant Staphylococcus aureus sequence type 398 (ST398) strain. This erm(T)-dfrK-tet(L) region was flanked by copies of the novel IS element ISSau10. The erm(T) region resembled that of Streptococcus pyogenes plasmid pRW35. The erm(T) gene of pKKS25 was expressed constitutively due to a 57-bp deletion in the erm(T) translational attenuator.

Genetics of antimicrobial resistance in Staphylococcus aureus

Strains of Staphylococcus aureus that are resistant to multiple antimicrobial compounds, including most available classes of antibiotics and some antiseptics, are a major threat to patient care owing to their stubborn intransigence to chemotherapy and disinfection. This reality has stimulated extensive efforts to understand the genetic nature of the determinants encoding antimicrobial resistance, together with the mechanisms by which these determinants evolve over time and are spread within bacterial populations. Such studies have benefited from the application of molecular genetics and in recent years, the sequencing of over a dozen complete staphylococcal genomes. It is now evident that the evolution of multiresistance is driven by the acquisition of discrete preformed antimicrobial resistance genes that are exchanged between organisms via horizontal gene transfer. Nonetheless, chromosomal mutation is the catalyst of novel resistance determinants and is likely to have an enhanced influence with the ongoing introduction of synthetic antibiotics.

Identification of a novel trimethoprim resistance gene, dfrK, in a methicillin-resistant Staphylococcus aureus ST398 strain and its physical linkage to the tetracycline resistance gene tet(L)

A novel trimethoprim resistance gene, designated dfrK, was detected in close proximity to the tetracycline resistance gene tet(L) on the ca. 40-kb plasmid pKKS2187 in a porcine methicillin (meticillin)-resistant Staphylococcus aureus isolate of sequence type 398. The dfrK gene encodes a 163-amino-acid dihydrofolate reductase that differs from all so-far-known dihydrofolate reductases.

Deletion of pT181-like sequence in an smr-encoding mosaic plasmid harboured by a persistent bovine Staphylococcus warneri strain

OBJECTIVES

The aim was to study the persistence and characteristics of Staphylococcus warneri strains resistant to quaternary ammonium compounds (QACs), including sequencing and analysis of two plasmids proved to carry the smr gene.

METHODS

During a 3.5 year period quarter milk samples were collected on three occasions from all lactating cows in a dairy herd. The samples were screened with regard to QAC-resistant bacteria using a selective medium. Thirty randomly selected QAC-resistant S. warneri were typed by PFGE and subjected to plasmid isolation and analysis followed by gene detection using PCR. Two smr-containing plasmids in S. warneri isolates were sequenced.

RESULTS

All isolates from the initial collection of quarter milk contained smr residing on a 5.8 kb plasmid (pSW174), which contained regions with high similarities to various plasmids, including pT181, pSK108 and pPI-2. The pT181-like sequence was flanked by 148 bp direct repeats, denoted ISLE49, with high similarity to previously reported sequences of approximately 148 bp, including ISLE39 flanking the insertion sequence IS257 in methicillin-resistant Staphylococcus aureus. All isolates from subsequent collections of quarter milk harboured a smaller smr-containing plasmid (pSW49). Sequence analyses revealed pSW49 (3552 bp) to be an in-part deleted version of pSW174 (5767 bp).

CONCLUSIONS

The IS-associated elements found in this study may have a wider role in the integration and excision of DNA sequences in staphylococci than previously reported. The mosaic plasmid structure based on genetic elements of various origins contributes to further knowledge on the flexibility of smr-encoding plasmids.

Staphylococcal tetracycline–MLSB resistance plasmid pSTE2 is the product of an RSA-mediated in vivo recombination

OBJECTIVES

The complete nucleotide sequence of the 6913 bp plasmid pSTE2 from Staphylococcus lentus, which mediates inducible resistance to tetracyclines, macrolides and lincosamides, was determined. The plasmid was analysed for potential reading frames and structural features to gain insight into its development from potential ancestor plasmids.

METHODS

Plasmid pSTE2 was transformed into Staphylococcus aureus RN4220. Suitable restriction fragments were cloned into E. coli plasmid vectors and sequenced. In vitro susceptibility testing was performed to confirm the resistance phenotype mediated by this plasmid.

RESULTS

Plasmid pSTE2 consisted of two parts, each of which corresponded closely to previously identified staphylococcal plasmids. The initial 4439 bp represented a pT181-analogous tet(K)-carrying tetracycline resistance plasmid, whereas the remaining 2474 bp represented a pPV141-related erm(C)-carrying macrolide-lincosamide-streptogramin B resistance plasmid. Both putative parental plasmids harboured the staphylococcal recombination site A (RSA) and the pT181-like plasmid also carried the recombinase gene pre whose product acts at RSA. Analysis of the junctions of the pT181-like and the pPV141-like homologous parts in pSTE2 suggested that plasmid pSTE2 developed from pT181- and pPV141-like ancestor plasmids by cointegrate formation at RSA.

CONCLUSION

Plasmid pSTE2 is the first completely sequenced plasmid from S. lentus and represents the product of an in vivo derived RSA-mediated recombination between two compatible plasmids.

Tetracycline resistance in staphylococci from free-living rodents and insectivores

One hundred and fifty-eight staphylococcal strains isolated from wild rodents and insectivores were analysed for plasmid-borne resistance to tetracycline (Tc). Only 10 isolates, six Staphylococcus saprophyticus isolates and single isolates of S. xylosus, S. equorum, S. warneri and S. cohnii subsp. cohnii carried a Tc resistance plasmid of approximately 4.4 kb as confirmed by protoplast transformation. All 10 plasmids harboured a Tc resistance gene of hybridization class K [tet(K)] as confirmed by polymerase chain reaction (PCR). The plasmid was assigned to the pT181 family as it revealed a high degree of restriction map homology to pT181 and other members of this family. Macrorestriction analysis with the enzyme SmaI showed that three of the six isolates identified as S. saprophyticus shared the same pulsed-field gel electrophoresis (PFGE) pattern.

Antibiotic resistance in food-related bacteria--a result of interfering with the global web of bacterial genetics

A series of antibiotic resistance genes have been sequenced and found to be identical or nearly identical in various ecological environments. Similarly, genetic vectors responsible for assembly and mobility of antibiotic resistance genes, such as transposons, integrons and R plasmids of similar or identical type are also widespread in various niches of the environment. Many zoonotic bacteria carry antibiotic resistance genes directly from different food-producing environments to the human being. These circumstances may have a major impact on the degree for success in treating infectious diseases in man. Several recent examples demonstrate that use of antibiotics in all parts of the food production chain contributes to the increasing level of antibiotic resistance among the food-borne pathogenic bacteria. Modern industrialized food production adds extra emphasis on lowering the use of antibiotics in all parts of agriculture, husbandry and fish farming because these food products are distributed to very large numbers of humans compared to more traditional smaller scale niche production.

Genetic linkage between resistance to quaternary ammonium compounds and beta-lactam antibiotics in food-related Staphylococcus spp

Little is known about the occurrence of antimicrobial resistance determinants in staphylococci isolated from food and food processing industries. Quaternary ammonium compound (QAC)-resistant coagulase-negative staphylococci (CNS) isolated from food and food-processing industries were investigated for the presence of genetic determinants (qacA/B and qacC/smr) encoding resistance to the QAC benzalkonium chloride (BC), several antibiotic resistance genes, and staphylococcal insertion sequences IS257 and IS256. Six qacA/B-harboring strains were resistant to penicillin and hybridized to a blaZ probe. The qacA/B and blaZ probes hybridized to plasmids of similar size in three isolates. Molecular and genetic characterization of the 23-kb plasmid (pST6) of Staphylococcus epidermidis St.6 revealed the presence of qacB adjacent to an incomplete beta-lactamase transposon Tn552 encoding the gene cluster blaZ, blaR, and blaI. Sequence analysis of flanking regions and the intergenic region between blaZ and qacB revealed the presence of IS257 downstream of blaZ as well as sin and binR between blaZ and qacB. In the three other BC and penicillin-resistant strains, the qacA/B and blaZ genes were located on separate plasmids. A qacC harboring S. epidermidis strain (St.17) also hybridized to tetK (tetracycline resistance) and ermB (erythromycin resistance) genes. The individual genes were located on separate plasmids, suggesting no linkage between QAC and antibiotic resistance determinants. Plasmid-free Staphylococcus aureus RN4220 allowed uptake of the pST6 plasmid DNA, indicating that the resistance genes could potentially be transferred to pathogens under selective stress. In conclusion, presence of both resistance determinants could lead to co-selection during antimicrobial therapy or disinfection in hospitals or in food industries.

Comparison of genes involved in penicillin resistance in staphylococci of bovine origin

Ten penicillin-resistant and -susceptible staphylococci, isolated from bovine mastitis milk, were studied for the presence of genes that are, or may be, involved in resistance against penicillin. The repressor (blaI), antirepressor (blaR1), and structural (blaZ) genes of the beta-lactamase-operon were found to be closely linked in all penicillin-resistant strains. The beta-lactamase gene cluster was more commonly located on chromosomal rather than plasmid DNA in the strains studied. The transposase (p480) gene, which has been identified in the Staphylococcus aureus beta-lactamase transposon Tn552, was found in only one single penicillin-resistant S. aureus strain. The other penicillin-resistant S. aureus isolates contained IS1181 in close location with the beta-lactamase gene cluster. In only one S. haemolyticus isolate was the beta-lactamase gene cluster found in close association with IS257. Penicillin-resistant S. aureus strains, which were additionally resistant to tetracycline, contained IS257 in close association with the tetracycline resistance gene (tetK). Sequence analysis of blaI, blaR1, and blaZ in two penicillin-resistant S. aureus strains revealed 94-96% sequence homology with bla in staphylococci of human origin. The results indicate a predominance of class I bla transposons rather than Tn3 family class II transposons in the isolates used in this study.

An IS257-derived hybrid promoter directs transcription of a tetA(K) tetracycline resistance gene in the Staphylococcus aureus chromosomal mec region

Transcription of the tetA(K) tetracycline resistance determinant encoded by an IS257-flanked cointegrated copy of a pT181-like plasmid, located within the chromosomal mec region of a methicillin-resistant Staphylococcus aureus isolate, has been investigated. The results demonstrated that transcription of tetA(K) in this strain is directed by both an IS257-derived hybrid promoter, which is stronger than the native tetA(K) promoter in the autonomous form of pT181, and a complete outwardly directed promoter identified within one end of IS257. Despite lower gene dosage, the chromosomal configuration was shown to afford a higher level of resistance than that mediated by pT181 in an autonomous multicopy state. Furthermore, competition studies revealed that a strain carrying the chromosomal tetA(K) determinant exhibited a higher level of fitness in the presence of tetracycline but not in its absence. This finding suggests that tetracycline has been a selective factor in the emergence of strains carrying a cointegrated pT181-like plasmid in their chromosomes. The results highlight the potential of IS257 to influence the expression of neighboring genes, a property likely to enhance its capacity to mediate advantageous genetic rearrangements.

Structural alterations in the translational attenuator of constitutively expressed ermC genes

Sequence deletions of 16, 59, and 111 bp as well as a tandem duplication of 272 bp with respect to the corresponding sequence of pT48 were identified in the regulatory regions of constitutively expressed ermC genes. Constitutive ermC gene expression as a consequence of these structural alterations is based on either the prevention of the formation of mRNA secondary structures in the translational attenuator or the preferential formation of those mRNA secondary structures which do not interfere with the translation of the ermC transcripts. A model for the development of sequence deletions in the ermC translational attenuator by homologous recombination is presented and experimentally tested by in vitro selection of constitutively expressed mutants in staphylococcal strains deficient and proficient in homologous recombination.

Mobile elements in the evolution and spread of multiple-drug resistance in staphylococci

Since the introduction of antimicrobial chemotherapy, staphylococci have shown a remarkable propensity to develop drug resistance. As a result, strains have evolved that are resistant to most classes of clinically useful antimicrobial agents. The emergence of these multiply-drug-resistant strains is primarily due to the capture of pre-existent resistance genes. In combination with plasmids and gene transfer mechanisms, mobile genetic elements have been central to the acquisition and dissemination of this resistance. In particular they have played a significant role in the assembly of drug-resistance gene clusters in these multiply-resistant staphylococci.