Sulfonamide resistance in Haemophilus influenzae mediated by acquisition of sul2 or a short insertion in chromosomal folP

A Hunt for the Resistance of Haemophilus influnezae to Beta-Lactams

Infections due to Haemophilus influnezae require prompt treatment using beta-lactam antibiotics. We used a collection of 81 isolates obtained between 1940 and 2001 from several countries. Whole genome sequencing showed the high heterogeneity of these isolates but allowed us to track the acquisition of beta-lactamase, which was first detected in 1980. Modifications of the ftsI gene encoding the penicillin-binding protein 3, PBP3, also involved in resistance to beta-lactams, appeared in 1991. These modifications (G490E, A502V, R517H, and N526K) were associated with resistance to amoxicillin that was not relieved by a beta-lactamase inhibitor (clavulanic acid), but the isolates retained susceptibility to third-generation cephalosporins (3GC). The modeling of the PBP3 structure suggested that these modifications may reduce the accessibility to the PBP3 active site. Other modifications appeared in 1998 and were associated with resistance to 3GC (S357N, M377I, S385T, and L389F). Modeling of the PBP3 structure suggested that they lie near the S379xN motif of the active site of PBP3. Overall resistance to amoxicillin was detected among 25 isolates (30.8%) of this collection. Resistance to sulfonamides was predicted by a genomic approach from the sequences of the folP gene (encoding the dihydropteroate synthase) due to difficulties in interpreting phenotypic anti-microbial testing and found in 13 isolates (16.0%). Our data suggest a slower spread of resistance to sulfonamides, which may be used for the treatment of H. influnezae infections. Genomic analysis may help in the prediction of antibiotic resistance, inform structure-function analysis, and guide the optimal use of antibiotics.

Spatiotemporal distribution, interactions and toxic effect of microorganisms and ARGs/MGEs from the bioreaction tank in hospital sewage treatment facility

Antibiotic resistance genes (ARGs) can be emitted from wastewater to ambient air and impose unignorable inhalable hazards, which could be exacerbated in antibiotic-concentrated hospital sewage. However, whether the ARG-carrying pathogens are more likely to infect cells remains largely unknown. Here, this study investigated and analyzed the spatiotemporal distribution, interaction, and toxicity of airborne microorganisms and their hosting ARGs in a hospital sewage treatment facility. The average concentration of ARGs/MGEs in sewage of bioreaction tank (BRT-W) was 2.27 × 104 gene copies/L. In the air of bioreaction tank (BRT-A), the average concentration of ARGs/MGEs was 15.86 gene copies/m3. In the four seasons, the ARGs concentration of sewage gradually decreased over time; The concentration of ARGs in the air first decreased and then increased. In spring, the concentration of ARGs/MGEs (qacedelta1-01) in BRT-W was highest (1.05 × 105 gene copies/L); The concentration of ARGs/MGEs (strB) in BRT-A in winter was higher than other seasons (26.18 gene copies/m3). Different from the past, this study also paid attention to the pathogenic potential of ARGs/MGEs in the air. The results of cell experiments showed that the cytotoxicity of drug-resistant Escherichia coli could reach Grade V. This suggested that the longer the drug-resistant E. coli were exposed to cells, the greater the cytotoxicity. Moreover, the cytotoxicity of bacteria increased with the increase in exposure time. In spring, the toxic effect of ARGs/MGEs in sewage of BRT-W was highest. Traceability analysis proved that BRT-W was an essential source of microorganisms and ARGs/MGEs in BRT-A. Furthermore, the combined risk of people exposed to the air of BRT in spring was higher than that in other seasons.

Analysis of random mutations in Salmonella Gallinarum dihydropteroate synthase conferring sulfonamide resistance

In bacteria and primitive eukaryotes, sulfonamide antibiotics block the folate pathway by inhibiting dihydropteroate synthase (FolP) that combines para-aminobenzoic acid (pABA) and dihydropterin pyrophosphate (DHPP) to form dihydropteroic acid (DHP), a precursor for tetrahydrofolate synthesis. However, the emergence of resistant strains has severely compromised the use of pABA mimetics as sulfonamide drugs. Salmonella enterica serovar Gallinarum (S. Gallinarum) is a significant source of antibiotic-resistant infections in poultry. Here, a sulfonamide-resistant FolP mutant library of S. Gallinarum was generated through random mutagenesis. Among resistant strains, substitution of amino acid Arginine 171 with Proline (R171P) in the FolP protein conferred the highest resistance against sulfonamide. Substitution of Phe28 with Leu or Ile (F28L/I) led to modest sulfonamide resistance. Structural modeling indicates that R171P and Phenylalanine 28 with leucine or isoleucine (F28L/I) substitution mutations are located far from the substrate-binding site and cause insignificant conformational changes in the FolP protein. Rather, in silico studies suggest that the mutations altered the stability of the protein, potentially resulting in sulfonamide resistance. Identification of specific mutations in FolP that confer resistance to sulfonamide would contribute to our understanding of the molecular mechanisms of antibiotic resistance.

Whole-Genome and Plasmid Comparative Analysis of Campylobacter jejuni from Human Patients in Toyama, Japan, from 2015 to 2019

Campylobacter jejuni is a major causative agent of food poisoning, and increasing antimicrobial resistance is a concern. This study investigated 116 clinical isolates of C. jejuni from Toyama, Japan, which were isolated from 2015 to 2019. Antimicrobial susceptibility testing and whole-genome sequencing were used for phenotypic and genotypic characterization to compare antimicrobial resistance (AMR) profiles and phylogenic linkage. The multilocus sequence typing approach identified 37 sequence types (STs) and 15 clonal complexes (CCs), including 7 novel STs, and the high frequency CCs were CC21 (27.7%), CC48 (10.9%), and CC354 (9.9%). The AMR profiles and related resistant factors were as follows: fluoroquinolones (51.7%), mutation in quinolone resistance-determining region (QRDRs) (GyrA T86I); tetracyclines (27.6%), acquisition of tet(O); ampicillin (7.8%), harboring bla_OXA184 or a promoter mutation in bla_OXA193; aminoglycosides (1.7%), acquisition of ant(6)-Ia and aph(3')-III; chloramphenicol (0.9%), acquisition of cat. The acquired resistance genes tet(O), ant(6)-Ia, aph(3')-III, and cat were located on pTet family plasmids. Furthermore, three pTet family plasmids formed larger plasmids that incorporated additional genes such as the type IV secretion system. Sequence type 4526 (ST4526; 10.9%), which is reported only in Japan, was the most predominant, suggesting continued prevalence. This study reveals the sequences of the pTet family plasmids harbored by C. jejuni in Japan, which had been unclear, and the acquisition of the insertion sequences in a part of the pTet family plasmids. Because pTet family plasmids can be horizontally transmitted and are a major factor in acquired resistance in Campylobacter, the risk of spreading pTet that has acquired further resistance should be considered. IMPORTANCE Campylobacter jejuni is among the major causes of enteritis and diarrhea in humans in many countries. Drug-resistant Campylobacter is increasing in both developing and developed countries, and in particular, fluoroquinolone-resistant Campylobacter was one of the species included on the priority list of antibiotic-resistant bacteria. Campylobacter drug resistance surveillance is important and has been conducted worldwide. In this study, we performed whole-genome analysis of Campylobacter jejuni isolated from diarrhea patients at a hospital in Toyama, Japan. This revealed the continued prevalence of Campylobacter jejuni ST4526, which has been reported to be prevalent in Japan, and the acquisition of resistance and virulence factors in the pTet family plasmids. The diversity of pTet family plasmids, the major resistance transmission factor, is expected to potentially increase the risk of Campylobacter. The usefulness of whole-genome sequencing in Campylobacter surveillance was also demonstrated.

Case Report: Whole-Genome Sequencing of Serially Collected Haemophilus influenzae From a Patient With Common Variable Immunodeficiency Reveals Within-Host Evolution of Resistance to Trimethoprim-Sulfamethoxazole and Azithromycin After Prolonged Treatment With These Antibiotics

We report within-host evolution of antibiotic resistance to trimethoprim-sulfamethoxazole and azithromycin in a nontypeable Haemophilus influenzae strain from a patient with common variable immunodeficiency (CVID), who received repeated or prolonged treatment with these antibiotics for recurrent respiratory tract infections. Whole-genome sequencing of three longitudinally collected sputum isolates during the period April 2016 to January 2018 revealed persistence of a strain of sequence type 2386. Reduced susceptibility to trimethoprim-sulfamethoxazole in the first two isolates was associated with mutations in genes encoding dihydrofolate reductase (folA) and its promotor region, dihydropteroate synthase (folP), and thymidylate synthase (thyA), while subsequent substitution of a single amino acid in dihydropteroate synthase (G225A) rendered high-level resistance in the third isolate from 2018. Azithromycin co-resistance in this isolate was associated with amino acid substitutions in 50S ribosomal proteins L4 (W59R) and L22 (G91D), possibly aided by a substitution in AcrB (A604E) of the AcrAB efflux pump. All three isolates were resistant to aminopenicillins and cefotaxime due to TEM-1B beta-lactamase and identical alterations in penicillin-binding protein 3. Further resistance development to trimethoprim-sulfamethoxazole and azithromycin resulted in a multidrug-resistant phenotype. Evolution of multidrug resistance due to horizontal gene transfer and/or spontaneous mutations, along with selection of resistant subpopulations is a particular risk in CVID and other patients requiring repeated and prolonged antibiotic treatment or prophylaxis. Such challenging situations call for careful antibiotic stewardship together with supportive and supplementary treatment. We describe the clinical and microbiological course of events in this case report and address the challenges encountered.

Genomic Diversity and Antimicrobial Resistance of Haemophilus Colonizing the Airways of Young Children with Cystic Fibrosis

Respiratory infection during childhood is a key risk factor in early cystic fibrosis (CF) lung disease progression. Haemophilus influenzae and Haemophilus parainfluenzae are routinely isolated from the lungs of children with CF; however, little is known about the frequency and characteristics of Haemophilus colonization in this context. Here, we describe the detection, antimicrobial resistance (AMR), and genome sequencing of H. influenzae and H. parainfluenzae isolated from airway samples of 147 participants aged ≤12 years enrolled in the Australian Respiratory Early Surveillance Team for Cystic Fibrosis (AREST CF) program, Melbourne, Australia. The frequency of colonization per visit was 4.6% for H. influenzae and 32.1% for H. parainfluenzae, 80.3% of participants had H. influenzae and/or H. parainfluenzae detected on at least one visit, and using genomic data, we estimate 15.6% of participants had persistent colonization with the same strain for at least two consecutive visits. Isolates were genetically diverse and AMR was common, with 52% of H. influenzae and 82% of H. parainfluenzae displaying resistance to at least one drug. The genetic basis for AMR could be identified in most cases; putative novel determinants include a new plasmid encoding blaTEM-1 (ampicillin resistance), a new inhibitor-resistant blaTEM allele (augmentin resistance), and previously unreported mutations in chromosomally carried genes (pbp3, ampicillin resistance; folA/folP, cotrimoxazole resistance; rpoB, rifampicin resistance). Acquired AMR genes were more common in H. parainfluenzae than H. influenzae (51% versus 21%, P = 0.0107) and were mostly associated with the ICEHin mobile element carrying blaTEM-1, resulting in more ampicillin resistance in H. parainfluenzae (73% versus 30%, P = 0.0004). Genomic data identified six potential instances of Haemophilus transmission between participants, of which three involved participants who shared clinic visit days. IMPORTANCE Cystic fibrosis (CF) lung disease begins during infancy, and acute respiratory infections increase the risk of early disease development and progression. Microbes involved in advanced stages of CF are well characterized, but less is known about early respiratory colonizers. We report the population dynamics and genomic determinants of AMR in two early colonizer species, namely, Haemophilus influenzae and Haemophilus parainfluenzae, collected from a pediatric CF cohort. This investigation also reveals that H. parainfluenzae has a high frequency of AMR carried on mobile elements that may act as a potential reservoir for the emergence and spread of AMR to H. influenzae, which has greater clinical significance as a respiratory pathogen in children. This study provides insight into the evolution of AMR and the colonization of H. influenzae and H. parainfluenzae in a pediatric CF cohort, which will help inform future treatment.

Genome-wide analysis of urogenital and respiratory multidrug-resistant Haemophilus parainfluenzae

OBJECTIVES

To characterize the mechanisms of antimicrobial resistance and the prevalence of the polysaccharide capsule among urogenital and respiratory Haemophilus parainfluenzae isolates.

METHODS

Antimicrobial susceptibility was tested by microdilution. Fifty-five MDR strains were subjected to WGS and were phylogenetically compared with all the available H. parainfluenzae genomes from the NCBI database. The identification of the capsular bexA gene was performed by PCR in 266 non-MDR strains.

RESULTS

In 31 of the 42 ampicillin-resistant strains, blaTEM-1 located within Tn3 was identified. β-Lactamase-negative cefuroxime-resistant strains (n = 12) presented PBP3 substitutions. The catS gene (n = 14), the tet(M)-MEGA element (n = 18) and FolA substitutions (I95L and F154V/S) (n = 41) were associated with resistance to chloramphenicol, tetracycline plus macrolides, and co-trimoxazole, respectively. Thirty-seven isolates had a Tn10 harbouring tet(B)/(C)/(D)/(R) genes with (n = 15) or without (n = 22) catA2. Putative transposons (Tn7076-Tn7079), including aminoglycoside and co-trimoxazole resistance genes, were identified in 10 strains (18.2%). These transposons were integrated into three new integrative and conjugative elements (ICEs), which also included the resistance-associated transposons Tn3 and Tn10. The capsular operon was found only in the urogenital isolates (18/154, 11.7%), but no phylogenetic clustering was observed. The capsular operons identified were similar to those of Haemophilus influenzae serotype c and Haemophilus sputorum type 2.

CONCLUSIONS

The identification of ICEs with up to three resistance-associated transposons suggests that these transferable elements play an important role in the acquisition of multidrug resistance in H. parainfluenzae. Moreover, the presence of polysaccharide capsules in some of these urogenital isolates is a cause for concern.

Effects of Sulfamethoxazole on the Microbial Community Dynamics During the Anaerobic Digestion Process

Anaerobic digestion (AD) treatment of cattle manure and slurry makes it possible to produce biogas, a renewable and storable biofuel, as well as digestate, a residual organic matter that can be used to replace chemical fertilizers. On the other hand, the intense use of antibiotics (e.g., sulfamethoxazole) in animal husbandry practices is showing increasing negative impacts resulting from the release of still metabolically active molecules into agroecosystems. In the present study, cattle manure collected from an AD plant-feeding tank was used as feedstock for AD experiments in which some batches were spiked with 5 mg L^-1 of sulfamethoxazole (SMX). Adding the antibiotic affected the microbial community dynamic; in particular, the efficiency of the acidogenic and acetogenic phases of the process corresponded to higher CH₄ and H₂ production than in the control. SMX was also degraded, and at the end of the experiment (69 days), just 20% of its initial concentration was found. The relative abundance (ARG/16S) of resistance genes sul1, sul2, and the proxy intI1 initially found in the ingestate decreased during the AD in both the spiked and control batches, suggesting that this process lowers the likelihood of antibiotic resistance genes spreading.

Role of Horizontal Gene Transfer in the Development of Multidrug Resistance in Haemophilus influenzae

Haemophilus influenzae colonizes the respiratory tract in humans and causes both invasive and noninvasive infections. As a threat to treatment, resistance against critically important antibiotics is on the rise in H. influenzae. Identifying mechanisms for horizontal acquisition of resistance genes is important to understand how multidrug resistance develops. The present study explores the antimicrobial resistance genes and their context in beta-lactam-resistant H. influenzae with coresistance to up to four non-beta-lactam groups. The results reveal that this organism is capable of acquiring resistance to a wide range of commonly used antibiotics through conjugative transfer of mobile genetic elements and transformation of chromosomal genes, resulting in mosaic genes with a broader resistance spectrum. Strains with chromosomally mediated resistance to extended-spectrum cephalosporins, co-trimoxazole, and quinolones combined with mobile genetic elements carrying genes mediating resistance to ampicillin, tetracyclines, and chloramphenicol have been reported, and further dissemination of such strains represents a particular concern.

Haemophilus influenzae colonizes the respiratory tract in humans and causes both invasive and noninvasive infections. Resistance to extended-spectrum cephalosporins in H. influenzae is rare in Europe. In this study, we defined acquired resistance gene loci and ftsI mutations in multidrug-resistant (MDR) and/or PBP3-mediated beta-lactam-resistant (rPBP3) H. influenzae strains, intending to understand the mode of spread of antibiotic resistance determinants in this species. Horizontal transfer of mobile genetic elements and transformation with resistance-conferring ftsI alleles were contributory. We found one small plasmid and three novel integrative conjugative elements (ICEs) which carry different combinations of resistance genes. Demonstration of transfer and/or ICE circular forms showed that the ICEs are functional. Two extensively MDR genetically unrelated H. influenzae strains (F and G) from the same geographical region shared an identical novel MDR ICE (Tn6686) harboring bla_TEM-1, catA2-like, and tet(B). The first Nordic case of MDR H. influenzae septicemia, strain 0, originating from the same geographical area as these strains, had a similar resistance pattern but contained another ICE [Tn6687 with bla_TEM-1, catP and tet(B)] with an overall structure quite similar to that of Tn6686. Comparison of the complete ftsI genes among rPBP3 strains revealed that the entire gene or certain regions of it are identical in genetically unrelated strains, indicating horizontal gene transfer. Our findings illustrate that H. influenzae is capable of acquiring resistance against a wide range of commonly used antibiotics through horizontal gene transfer, in terms of conjugative transfer of ICEs and transformation of chromosomal genes.

IMPORTANCEHaemophilus influenzae colonizes the respiratory tract in humans and causes both invasive and noninvasive infections. As a threat to treatment, resistance against critically important antibiotics is on the rise in H. influenzae. Identifying mechanisms for horizontal acquisition of resistance genes is important to understand how multidrug resistance develops. The present study explores the antimicrobial resistance genes and their context in beta-lactam-resistant H. influenzae with coresistance to up to four non-beta-lactam groups. The results reveal that this organism is capable of acquiring resistance to a wide range of commonly used antibiotics through conjugative transfer of mobile genetic elements and transformation of chromosomal genes, resulting in mosaic genes with a broader resistance spectrum. Strains with chromosomally mediated resistance to extended-spectrum cephalosporins, co-trimoxazole, and quinolones combined with mobile genetic elements carrying genes mediating resistance to ampicillin, tetracyclines, and chloramphenicol have been reported, and further dissemination of such strains represents a particular concern.

Assessment of trimethoprim-sulfamethoxazole susceptibility testing methods for fastidious Haemophilus spp

OBJECTIVES

To compare the determinants of trimethoprim-sulfamethoxazole resistance with established susceptibility values for fastidious Haemophilus spp., to provide recommendations for optimal trimethoprim-sulfamethoxazole measurement.

METHODS

We collected 50 strains each of Haemophilus influenzae and Haemophilus parainfluenzae at Bellvitge University Hospital. Trimethoprim-sulfamethoxazole susceptibility was tested by microdilution, E-test and disc diffusion using both Mueller-Hinton fastidious (MH-F) medium and Haemophilus test medium (HTM) following EUCAST and CLSI criteria, respectively. Mutations in folA, folP and additional determinants of resistance were identified in whole-genome-sequenced isolates.

RESULTS

Strains presented generally higher rates of trimethoprim-sulfamethoxazole resistance when grown on HTM than on MH-F, independent of the methodology used (average MIC 2.6-fold higher in H. influenzae and 1.2-fold higher in H. parainfluenzae). The main resistance-related determinants were as follows: I95L and F154S/V in folA; 3- and 15-bp insertions and substitutions in folP; acquisition of sul genes; and FolA overproduction potentially linked to mutations in -35 and -10 promoter motifs. Of note, 2 of 19 H. influenzae strains (10.5%) and 9 of 33 H. parainfluenzae strains (27.3%) with mutations and assigned as resistant by microdilution were inaccurately considered susceptible by disc diffusion. This misinterpretation was resolved by raising the clinical resistance breakpoint of the EUCAST guidelines to ≤30 mm.

CONCLUSIONS

Given the routine use of disc diffusion, a significant number of strains could potentially be miscategorized as susceptible to trimethoprim-sulfamethoxazole despite having resistance-related mutations. A simple modification to the current clinical resistance breakpoint given by the EUCAST guideline for MH-F ensures correct interpretation and correlation with the reference standard method of microdilution.

Dissipation of the antibiotic sulfamethoxazole in a soil amended with anaerobically digested cattle manure

The application of anaerobically digested cattle manure on agricultural land for both improving its quality and recycling a farm waste is an increasingly frequent practice in line with the circular economy. However, knowledge on the potential risk of spreading antibiotic resistance through this specific practice is quite scarce. The antibiotic sulfamethoxazole (SMX) is one of the most heavily prescribed in veterinary medicine. In this study, SMX dissipation and the possible effects on natural microorganisms were investigated in a soil amended with an anaerobically digested cattle manure produced from a biogas plant inside a livestock farm. Microcosm experiments were performed using amended soil treated with SMX (20 mg/kg soil). During the experimental time (61 days), soil samples were analysed for SMX and N4-acetylsulfamethoxazole, microbial abundance, activity and structure. Furthermore, the prevalence of the intI1 gene was also determined. The overall results showed that, although there was an initial negative effect on microbial abundance, SMX halved in about 7 days in the digestate-amended soil. The intI1 gene found in both the digestate and amended soil suggested that the use of anaerobically digested cattle manure as fertilizer can be a source of antibiotic resistant bacteria (ARBs) and genes (ARGs) in agroecosystems.

Antimicrobial Resistance in Pasteurellaceae of Veterinary Origin

Members of the highly heterogeneous family Pasteurellaceae cause a wide variety of diseases in humans and animals. Antimicrobial agents are the most powerful tools to control such infections. However, the acquisition of resistance genes, as well as the development of resistance-mediating mutations, significantly reduces the efficacy of the antimicrobial agents. This article gives a brief description of the role of selected members of the family Pasteurellaceae in animal infections and of the most recent data on the susceptibility status of such members. Moreover, a review of the current knowledge of the genetic basis of resistance to antimicrobial agents is included, with particular reference to resistance to tetracyclines, β-lactam antibiotics, aminoglycosides/aminocyclitols, folate pathway inhibitors, macrolides, lincosamides, phenicols, and quinolones. This article focusses on the genera of veterinary importance for which sufficient data on antimicrobial susceptibility and the detection of resistance genes are currently available (Pasteurella, Mannheimia, Actinobacillus, Haemophilus, and Histophilus). Additionally, the role of plasmids, transposons, and integrative and conjugative elements in the spread of the resistance genes within and beyond the aforementioned genera is highlighted to provide insight into horizontal dissemination, coselection, and persistence of antimicrobial resistance genes. The article discusses the acquisition of diverse resistance genes by the selected Pasteurellaceae members from other Gram-negative or maybe even Gram-positive bacteria. Although the susceptibility status of these members still looks rather favorable, monitoring of their antimicrobial susceptibility is required for early detection of changes in the susceptibility status and the newly acquired/developed resistance mechanisms.

Spatiotemporal profile of tetracycline and sulfonamide and their resistance on a catchment scale

Tetracyclines and sulfonamides are the two classes of antibiotics commonly used in the medical, industrial and agricultural activities. Their extensive usage has caused the proliferation and propagation of resistant bacteria (ARB) and resistance genes (ARGs) in the environment. In this study, the occurrence and distribution of tetracyclines (TC, OTC and CTC) and sulfonamides (SMX, SCX and TMP), their associated ARB and ARGs were quantified in water and sediments collected from the mainstream of Liaohe River, northeast China. The average concentration of tetracyclines was higher in May, while the concentration of sulfonamides was slightly higher in October. The highest concentrations of the total tetracyclines and sulfonamides in sediments were 2.7×10³ ng/g and 2.1×10² ng/g respectively detected in May. All detected ARGs were found generally with high abundance. The tetA, tetB and tetE genes were dominant (4.4×10^-2 to 9.8×10^-1 copies of tet genes/copies of 16S rRNA genes) in total communities, and the average abundance of sul genes was expressed above 10^-1 in the water samples in May and October. Redundance analysis (RDA) and principle component analysis (PCA) indicated that the antibiotic residue was the most important contributor to the level of tetracycline and sulfonamide resistance genes, and some hydrogeological conditions (e.g. flow rate, intersection settlement) influenced the distribution of resistance genes. Results from this study could help understand the proliferation and propagation of antibiotic resistance on a river catchment scale and mitigate the potential risks to public health.

A Comparison of Genotypic and Phenotypic Methods for Analyzing the Susceptibility to Sulfamethoxazole and Trimethoprim in Edwardsiella piscicida

In a study of 39 isolates of Edwardsiella piscicida made from Korean aquaculture sites, sul genes were detected in 16 isolates and dfr genes in 19. Ten isolates were shown to contain both sul and dfr genes. MIC and disc diffusion zones assays were performed to measure the phenotypic susceptibilities of the 39 isolates. Normalized resistance interpretation was applied to these data to categorize isolates as either fully susceptible or as manifesting reduced susceptibility. The standard CLSI protocols specify the use of a mixture of sulfamethoxazole/trimethoprim (20:1) in both MIC and disc diffusion tests. Using the CLSI MIC protocol, 100% of the isolates containing dfr genes, but only 75% of the isolates containing sul genes, were categorized as manifesting reduced susceptibility. Using the CLSI disc diffusion protocol, only 58% of the isolates containing dfr genes and 69% of those containing sul genes were categorized as manifesting reduced susceptibility. When the single agent trimethoprim was substituted for the combined mixture in both the MIC and disc diffusion protocols, 100% of the dfr-positive isolates were categorized as NWT. When the single-agent sulfamethoxazole was substituted, the analysis of the MIC characterized 100% and the disc zone data 94% of the sul-positive isolates as manifesting reduced susceptibility. It is argued that the use of trimethoprim and sulfamethoxazole as single agents in phenotypic susceptibility tests would provide more meaningful data than the currently recommended use of these two agents combined.

Inactivation of the Thymidylate Synthase thyA in Non-typeable Haemophilus influenzae Modulates Antibiotic Resistance and Has a Strong Impact on Its Interplay with the Host Airways

Antibacterial treatment with cotrimoxazol (TxS), a combination of trimethoprim and sulfamethoxazole, generates resistance by, among others, acquisition of thymidine auxotrophy associated with mutations in the thymidylate synthase gene thyA, which can modify the biology of infection. The opportunistic pathogen non-typeable Haemophilus influenzae (NTHi) is frequently encountered in the lower airways of chronic obstructive pulmonary disease (COPD) patients, and associated with acute exacerbation of COPD symptoms. Increasing resistance of NTHi to TxS limits its suitability as initial antibacterial against COPD exacerbation, although its relationship with thymidine auxotrophy is unknown. In this study, the analysis of 2,542 NTHi isolates recovered at Bellvitge University Hospital (Spain) in the period 2010–2014 revealed 119 strains forming slow-growing colonies on the thymidine low concentration medium Mueller Hinton Fastidious, including one strain isolated from a COPD patient undergoing TxS therapy that was a reversible thymidine auxotroph. To assess the impact of thymidine auxotrophy in the NTHi-host interplay during respiratory infection, thyA mutants were generated in both the clinical isolate NTHi375 and the reference strain RdKW20. Inactivation of the thyA gene increased TxS resistance, but also promoted morphological changes consistent with elongation and impaired bacterial division, which altered H. influenzae self-aggregation, phosphorylcholine level, C3b deposition, and airway epithelial infection patterns. Availability of external thymidine contributed to overcome such auxotrophy and TxS effect, potentially facilitated by the nucleoside transporter nupC. Although, thyA inactivation resulted in bacterial attenuation in a lung infection mouse model, it also rendered a lower clearance upon a TxS challenge in vivo. Thus, our results show that thymidine auxotrophy modulates both the NTHi host airway interplay and antibiotic resistance, which should be considered at the clinical setting for the consequences of TxS administration.

Characterization of Integrons and Sulfonamide Resistance Genes among Bacteria from Drinking Water Distribution Systems in Southwestern Nigeria

BACKGROUND

The emergence of antibiotic resistance among pathogenic bacteria in clinical and environmental settings is a global problem. Many antibiotic resistance genes are located on mobile genetic elements such as plasmids and integrons, enabling their transfer among a variety of bacterial species. Water distribution systems may be reservoirs for the spread of antibiotic resistance.

MATERIALS AND METHODS

Bacteria isolated from raw, treated, and municipal tap water samples from selected water distribution systems in south-western Nigeria were investigated using the point inoculation method with seeded antibiotics, PCR amplification, and sequencing for the determination of bacterial resistance profiles and class 1/2 integrase genes and gene cassettes, respectively.

RESULTS

sul1,sul2, and sul3 were detected in 21.6, 27.8, and 0% of the isolates, respectively (n = 162). Class 1 and class 2 integrons were detected in 21.42 and 3.6% of the isolates, respectively (n = 168). Genes encoding resistance to aminoglycosides (aadA2, aadA1, and aadB), trimethoprim (dfrA15, dfr7, and dfrA1), and sulfonamide (sul1) were detected among bacteria with class 1 integrons, while genes that encodes resistance to strepthothricin (sat2) and trimethoprim (dfrA15) were detected among bacteria with class 2 integrons.

CONCLUSIONS

Bacteria from these water samples are a potential reservoir of multidrug-resistant traits including sul genes and mobile resistance elements, i.e. the integrase gene.

Antibiogram of Stenotrophomonas maltophilia Isolated From Nkonkobe Municipality, Eastern Cape Province, South Africa

Background:

Assessment of resistance genes is imperative, as they become disseminated to bacterial flora in plants and to the indigenous bacterial community, and thus ultimately contributes to the clinical problems of antibiotic resistant pathogens.

Objectives:

The research was to assess the antibiotic characteristics and incidence of sul3 genes of Stenotrophomonas maltophilia isolates recovered from rhizospheres plant in Nkonkobe Municipality.

Materials and Methods:

Identification and assessment of resistance genes (sul2 and sul3 genes) were carried out using polymerase chain reaction (PCR). Analytical profile index (API) was used for biochemical characterization for identification before the PCR. Antibiotic susceptibility test was carried out using the approved guidelines and standards of Clinical Laboratory Standard Institute (CLSI).

Results:

A total of 125 isolates were identified, composed of 120 (96%) from grass root rhizosphere and 5 (4%) from soil butternut root rhizosphere. In vitro antibiotic susceptibility tests showed varying resistances to meropenem (8.9%), cefuroxime (95.6 %), ampicillin-sulbactam (53.9%), ceftazidime (10.7%), cefepime (29.3 %), minocycline (2.2%), kanamycin (56.9%), ofloxacin (2.9%), levofloxacin (1.3%), moxifloxacin (2.8%), ciprofloxacin (24.3%), gatifloxacin (1.3%), polymyxin B (2.9 %), cotrimoxazole (26.1%), trimethoprim (98.6%) and aztreonam (58%). The isolates were susceptible to the fluoroquinolones (74.3-94.7%), polymycin (97.1%) and meropenem (88.1%). The newest sulphonamide resistance gene, sul3, was detected among the trimethoprim-sulfamethoxazole (cotrimoxazole)-resistant isolates, while the most frequent sulphonamide-resistant gene in animal source isolates, sul2, was not.

Conclusions:

The commensal S. maltophilia isolates in the Nkonkobe Municipality environment harbored the resistant gene sul3 as clinical counterparts, especially from the perspective of reservoirs of antibiotic resistance determinants.

Sulfonamide antibiotics in the Northern Yellow Sea are related to resistant bacteria: implications for antibiotic resistance genes

Antibiotic resistance gene (ARG) residues and the mode of transmission in marine environments remain unclear. The sulfonamide (SAs) concentrations, different genes and total bacterial abundance in seawater and sediment of the Northern Yellow Sea were analyzed. Results showed the genes sul I and sul II were present at relatively high concentrations in all samples, whereas the gene sul III was detected fewer. The ARGs concentrations in the sediment were 10(3) times higher than those in water, which indicated sediment was essential ARG reservoir. Statistical analysis revealed the total antibiotic concentration was positively correlated with the relative abundance of the gene sul I and sul II. The relative abundances of the gene sul I and the gene sul II were also correlated positively with those of the gene int1. This correlation demonstrated that SAs exerted selective pressure on these ARGs, whereas the gene int1 could be implicated in the propagation of the genes sul I and sul II in marine environments.

Aerobic biodegradation of the sulfonamide antibiotic sulfamethoxazole by activated sludge applied as co-substrate and sole carbon and nitrogen source

Potential aerobic biodegradation mechanisms of the widely used polar, low-adsorptive sulfonamide antibiotic sulfamethoxazole (SMX) were investigated in activated sludge at bench scale. The study focused on (i) SMX co-metabolism with acetate and ammonium nitrate and (ii) SMX utilization when present as the sole carbon and nitrogen source. With SMX adsorption being negligible, elimination was primarily based on biodegradation. Activated sludge was able to utilize SMX both as a carbon and/or nitrogen source. SMX biodegradation was enhanced when a readily degradable energy supply (acetate) was provided which fostered metabolic activity. Moreover, it was raised under nitrogen deficiency conditions. The mass balance for dissolved organic carbon showed an incomplete SMX mineralization with two scenarios: (i) with SMX as a co-substrate, 3-amino-5-methyl-isoxazole represented the main stable metabolite and (ii) SMX as sole carbon and nitrogen source possibly yielded hydroxyl-N-(5-methyl-1,2-oxazole-3-yl)benzene-1-sulfonamide as a further metabolite.

Occurrence of sulfonamide and tetracycline-resistant bacteria and resistance genes in aquaculture environment

The occurrence of sulfonamide and tetracycline resistance and their pollution profile in the aquaculture environment of Tianjin, northern China, were investigated. The presence of antibiotic-resistant bacteria was identified and the corresponding antibiotic resistance genes (ARGs) were quantified at 6 aquaculture farms in Tianjin. Sulfonamide-resistance genes were prevalent and their concentrations were the highest detected (3.0 × 10(-5) to 3.3 × 10(-4) for sul1/16S rDNA, 2.0 × 10(-4) to 1.8 × 10(-3) for sul2/16S rDNA) among the various ARGs, most likely because the use of sulfonamides is more prevalent than tetracyclines in this area. Bacillus was the most dominant bacterial genus in both sulfamethoxazole resistant bacteria (63.27% of the total resistant bacteria) and tetracycline-resistant bacteria (57.14% of the total resistant bacteria). At least two of those genes (tetM, tetO, tetT, tetW, sul1 and sul2) were detected in the isolates of Bacillus cereus, Bacillus subtilis, Bacillus megaterium and Acinetobacter lwofii, and all of the above genes were detected in B. cereus, suggesting the occurrence of multi-resistance in the studied area. The genetic transfer of sul1 between intestinal bacteria (e.g., Enterococcus spp.) and indigenous bacteria (e.g., Bacillus spp.) was implied by phylogenetic analysis. Several strains of resistant opportunistic pathogens (e.g., Acinetobacter spp.) were found in indigenous bacteria, which increase the risk of ARGs to public health. Overall, this is the first study to comprehensively investigate the antibiotic resistance profile by analyzing the species of antibiotic-resistant bacteria and adopting qualitative and quantitative methods to investigate ARGs at a typical aquaculture area in northern China.

Distribution of quinolones, sulfonamides, tetracyclines in aquatic environment and antibiotic resistance in indochina

Southeast Asia has become the center of rapid industrial development and economic growth. However, this growth has far outpaced investment in public infrastructure, leading to the unregulated release of many pollutants, including wastewater-related contaminants such as antibiotics. Antibiotics are of major concern because they can easily be released into the environment from numerous sources, and can subsequently induce development of antibiotic-resistant bacteria. Recent studies have shown that for some categories of drugs this source-to-environment antibiotic resistance relationship is more complex. This review summarizes current understanding regarding the presence of quinolones, sulfonamides, and tetracyclines in aquatic environments of Indochina and the prevalence of bacteria resistant to them. Several noteworthy findings are discussed: (1) quinolone contamination and the occurrence of quinolone resistance are not correlated; (2) occurrence of the sul sulfonamide resistance gene varies geographically; and (3) microbial diversity might be related to the rate of oxytetracycline resistance.

Antibiotic contamination and occurrence of antibiotic-resistant bacteria in aquatic environments of northern Vietnam

The ubiquitous application and release of antibiotics to the environment can result in bacterial antibiotic resistance, which in turn can be a serious risk to humans and other animals. Southeast Asian countries commonly apply an integrated recycling farm system called VAC (Vegetable, Aquaculture and Caged animal). In the VAC environment, antibiotics are released from animal and human origins, which would cause antibiotic-resistant bacteria (ARB). This study evaluated occurrence of ARB in the VAC environment in northern Vietnam, with quantitative analysis of antibiotic pollution. We found that sulfonamides were commonly detected at all sites. In dry season, while sulfamethazine was a major contaminant in pig farm pond (475-6662 ng/l) and less common in city canal and aquaculture sites, sulfamethoxazole was a major one in city canal (612-4330 ng/l). Erythromycin (154-2246 ng/l) and clarithromycin (2.8-778 ng/ml) were the common macrolides in city canal, but very low concentrations in pig farm pond and aquaculture sites. High frequencies of sulfamethoxazole-resistant bacteria (2.14-94.44%) were found whereas the occurrence rates of erythromycin-resistant bacteria were lower (<0.01-38.8%). A positive correlation was found between sulfamethoxazole concentration and occurrence of sulfamethoxazole-resistant bacteria in dry season. The sulfamethoxazole-resistant isolates were found to belong to 25 genera. Acinetobacter and Aeromonas were the major genera. Twenty three of 25 genera contained sul genes. This study showed specific contamination patterns in city and VAC environments and concluded that ARB occurred not only within contaminated sites but also those less contaminated. Various species can obtain resistance in VAC environment, which would be reservoir of drug resistance genes. Occurrence of ARB is suggested to relate with rainfall condition and horizontal gene transfer in diverse microbial community.

Trends in antibiotic resistance genes occurrence in the Haihe River, China

The occurrence of antibiotics and antibiotic resistance genes (ARGs) was quantified in water and sediment samples collected from a 72 km stretch of the Haihe River, China. Tetracycline resistance genes (tetW, tetQ, tetO, tetT, tetM, tetB, and tetS) were not detected by quantitative PCR in many samples. In contrast, sul1 and sul2 (coding for sulfonamide resistance) were present at relatively high concentrations in all (38) samples. The highest ARG concentrations detected were (7.8 ± 1.0) × 10(9) copies/g for sul1 and (1.7 ± 0.2) × 10(11) copies/g for sul2, in sediment samples collected during the summer. The corresponding total bacterial concentration (quantified with a universal 16S-rDNA probe) was (3.3 ± 0.4) × 10(12) cells/g. Sul1 and sul2 concentrations in sediments were 120-2000 times higher than that in water, indicating that sediments are an important ARG reservoir in the Haihe River. Statistical analysis indicated a positive correlation between the relative abundance of these ARGs (i.e., sul1/16S-rDNA and sul2/16S-rDNA) and the total concentration of sulfamethoxazole, sulfadiazine, plus sulfachlororyridazine, suggesting that sulfonamides exerted selective pressure for these ARGs. A class 1 integron was implicated in the propagation of sul1. Overall, the widespread distribution of sulfonamide ARGs underscores the need to better understand and mitigate their propagation in the environment and the associated risks to public health.

Detection of the sul1, sul2, and sul3 genes in sulfonamide-resistant bacteria from wastewater and shrimp ponds of north Vietnam

To assess the presence and distribution of the sul genes (sul1, sul2, and sul3) and plasmids in human-mediated environments of north Vietnam, we examined a total of 127 sulfonamide-resistant (SR) bacterial isolates from four shrimp ponds (HNAQs), a city canal (HNCs) and three fish ponds that received wastewater directly from swine farms (HNPs). Results from the SR isolates revealed that sul genes were most frequently detected in the HNPs (92.0%), followed by HNCs (72.0%), and the HNAQs (43.0%). Among the sul genes detected, sul1 was the most prevalent gene in all three environments (57.0, 33.0 and 60.0% in HNPs, HNAQs, and HNCs, respectively) followed by sul2 (51.0, 19.0, and 20.0%, respectively) and sul3 (14.0, 6.0, and 8.0%, respectively). All combinations of paired different sul genes were detected, with the combination between sul1 and sul2 being the most frequent in all three environments (20.0, 8.0, and 8.0% in HNPs, HNAQs, and HNCs, respectively). The combination of three sul genes was detected at low frequencies (2-3%) in the HNPs and HNAQs, and was absent in the HNCs. The sul genes were more frequently located on the chromosome than on plasmids. The identification of SR isolates positive for the sul genes and plasmids showed that Acinetobacter was the most dominant. Our study revealed that the sul genes were common in SR bacteria from the aquatic environments we examined from northern Vietnam. Wastewater from swine farms might be "hot spots" of the sul genes and plasmids and may be reservoirs for the exchange of the sul genes among bacteria.

Crystal Structure of 7,8-Dihydropteroate Synthase from Bacillus anthracis

Dihydropterate synthase (DHPS) is the target for the sulfonamide class of antibiotics, but increasing resistance has encouraged the development of new therapeutic agents against this enzyme. One approach is to identify molecules that occupy the pterin binding pocket which is distinct from the pABA binding pocket that binds sulfonamides. Toward this goal, we present five crystal structures of DHPS from Bacillus anthracis, a well-documented bioterrorism agent. Three DHPS structures are already known, but our B. anthracis structures provide new insights into the enzyme mechanism. We show how an arginine side chain mimics the pterin ring in binding within the pterin binding pocket. The structures of two substrate analog complexes and the first structure of a DHPS-product complex offer new insights into the catalytic mechanism and the architecture of the pABA binding pocket. Finally, as an initial step in the development of pterin-based inhibitors, we present the structure of DHPS complexed with 5-nitro-6-methylamino-isocytosine.

Mutations and horizontal transmission have contributed to sulfonamide resistance in Streptococcus pyogenes

Two variants of dihydropteroate synthase (DHPS) were found among sulfonamide-resistant Streptococcus pyogenes, one of which was characterized by a 2-amino-acid addition in a conserved part of the enzyme. The enzyme kinetics of both variants was compared with the kinetics of DHPS from a sulfonamide-susceptible S. pyogenes. The most striking difference was a substantially elevated Ki for both variants, but variations in Km for both of its substrates p-aminobenzoic acid (p-AB) and dihydropteridine-pyrophosphate (pteridine) were also found. In the resistance variant lacking additions, the amino acid at position 213 was changed by site-directed mutagenesis from a Gly to an Arg, which resulted in a lower Ki. The corresponding change from an Arg to a Gly in the DHPS from a susceptible isolate led to a substantially increased Ki, confirming the importance of this amino acid difference for the resistance. Nucleotide sequence determinations of the complete folate operon revealed in some isolates a mosaic pattern of differences compared to the wild type, not only in the genes coding for DHPS and GTP cyclohydrolase (GTPCH) noted earlier but also in genes coding for dihydroneopterin aldolase (DHNA) and hydroxymethylpterin pyrophosphokinase (HPPK). Regions of sequence differences were interspersed with regions of complete identity in a mosaic pattern, indicating a dispersed pattern of uptake of foreign DNA in the resistant isolates.

Worldwide trends in antimicrobial resistance among common respiratory tract pathogens in children

BACKGROUND

Respiratory tract infections among children are a common reason for health care provider visits and the primary reason for antimicrobial prescribing in this population. The increased prevalence of resistance among Streptococcus pneumoniae and Haemophilus influenzae pathogens poses a serious challenge in the successful treatment of respiratory tract infections caused by these pathogens.

METHODS

This paper reviews worldwide trends in antimicrobial resistance among common respiratory tract pathogens, highlighting data obtained from the pediatric population where available.

RESULTS

S. pneumoniae resistance to beta-lactams is mediated through alterations in the penicillin-binding proteins and macrolide resistance to acquisition of efflux or methylation genes. The mechanisms of resistance to the fluoroquinolones include target enzyme alterations via genetic mutations and transport out of the bacterial cell via an efflux pump. Beta-lactamase production is the primary mechanism of resistance to penicillins among H. influenzae isolates. Although S. pneumoniae with reduced susceptibility to penicillin was first documented > 30 years ago, resistance has increased at an alarming rate worldwide in the past decade. According to recent surveillance data, the worldwide prevalence of S. pneumoniae with reduced susceptibility to penicillin is 18.2%. Beta-lactamase production among H. influenzae ranges from approximately 4% in Russia to 26% in the United States and to 31% in France. The prevalence of beta-lactamase-negative, ampicillin-resistant H. influenzae remains very low (< 1%) worldwide, except in Japan, where the incidence is higher. In general, the highest rates of resistance are observed in isolates obtained from children, and risk factors for infection with a resistant pathogen include young age, the site of infection, day-care center attendance and recent antimicrobial use.

CONCLUSIONS

Increased prevalence of antimicrobial resistance among respiratory tract pathogens isolated from children and adults is evident worldwide. Treatment of infections caused by S. pneumoniae and H. influenzae with older agents or ineffective dosing regimens may not eradicate infections and may contribute to the spread of resistance. These observations confirm the need for appropriate antimicrobial use to halt or at least limit the spread of resistance.