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Pham NP, Gingras H, Godin C, Feng J, Groppi A, Nikolski M, Leprohon P, Ouellette M. Holistic understanding of trimethoprim resistance in Streptococcus pneumoniae using an integrative approach of genome-wide association study, resistance reconstruction, and machine learning. mBio 2024; 15:e0136024. [PMID: 39120145 PMCID: PMC11389379 DOI: 10.1128/mbio.01360-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Accepted: 07/08/2024] [Indexed: 08/10/2024] Open
Abstract
Antimicrobial resistance (AMR) is a public health threat worldwide. Next-generation sequencing (NGS) has opened unprecedented opportunities to accelerate AMR mechanism discovery and diagnostics. Here, we present an integrative approach to investigate trimethoprim (TMP) resistance in the key pathogen Streptococcus pneumoniae. We explored a collection of 662 S. pneumoniae genomes by conducting a genome-wide association study (GWAS), followed by functional validation using resistance reconstruction experiments, combined with machine learning (ML) approaches to predict TMP minimum inhibitory concentration (MIC). Our study showed that multiple additive mutations in the folA and sulA loci are responsible for TMP non-susceptibility in S. pneumoniae and can be used as key features to build ML models for digital MIC prediction, reaching an average accuracy within ±1 twofold dilution factor of 86.3%. Our roadmap of in silico analysis-wet-lab validation-diagnostic tool building could be adapted to explore AMR in other combinations of bacteria-antibiotic. IMPORTANCE In the age of next-generation sequencing (NGS), while data-driven methods such as genome-wide association study (GWAS) and machine learning (ML) excel at finding patterns, functional validation can be challenging due to the high numbers of candidate variants. We designed an integrative approach combining a GWAS on S. pneumoniae clinical isolates, followed by whole-genome transformation coupled with NGS to functionally characterize a large set of GWAS candidates. Our study validated several phenotypic folA mutations beyond the standard Ile100Leu mutation, and showed that the overexpression of the sulA locus produces trimethoprim (TMP) resistance in Streptococcus pneumoniae. These validated loci, when used to build ML models, were found to be the best inputs for predicting TMP minimal inhibitory concentrations. Integrative approaches can bridge the genotype-phenotype gap by biological insights that can be incorporated in ML models for accurate prediction of drug susceptibility.
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Affiliation(s)
- Nguyen-Phuong Pham
- Centre de Recherche en Infectiologie du Centre de Recherche du CHU de Québec and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec City, Québec, Canada
| | - Hélène Gingras
- Centre de Recherche en Infectiologie du Centre de Recherche du CHU de Québec and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec City, Québec, Canada
| | - Chantal Godin
- Centre de Recherche en Infectiologie du Centre de Recherche du CHU de Québec and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec City, Québec, Canada
| | - Jie Feng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Alexis Groppi
- Bordeaux Bioinformatics Center and CNRS, Institut de Biochimie et Génétique Cellulaires (IBGC) UMR 5095, Université de Bordeaux, Bordeaux, France
| | - Macha Nikolski
- Bordeaux Bioinformatics Center and CNRS, Institut de Biochimie et Génétique Cellulaires (IBGC) UMR 5095, Université de Bordeaux, Bordeaux, France
| | - Philippe Leprohon
- Centre de Recherche en Infectiologie du Centre de Recherche du CHU de Québec and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec City, Québec, Canada
| | - Marc Ouellette
- Centre de Recherche en Infectiologie du Centre de Recherche du CHU de Québec and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec City, Québec, Canada
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Gingras H, Peillard-Fiorente F, Godin C, Patron K, Leprohon P, Ouellette M. New Resistance Mutations Linked to Decreased Susceptibility to Solithromycin in Streptococcus pneumoniae Revealed by Chemogenomic Screens. Antimicrob Agents Chemother 2023; 67:e0039523. [PMID: 37409958 PMCID: PMC10433811 DOI: 10.1128/aac.00395-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 06/18/2023] [Indexed: 07/07/2023] Open
Abstract
Two strains of Streptococcus pneumoniae, one expressing the methyltransferase Erm(B) and the other negative for erm(B), were selected for solithromycin resistance in vitro either with direct drug selection or with chemical mutagenesis followed by drug selection. We obtained a series of mutants that we characterized by next-generation sequencing. We found mutations in various ribosomal proteins (L3, L4, L22, L32, and S4) and in the 23S rRNA. We also found mutations in subunits of the phosphate transporter, in the DEAD box helicase CshB, and in the erm(B)L leader peptide. All mutations were shown to decrease solithromycin susceptibility when transformed into sensitive isolates. Some of the genes derived from our in vitro screens were found to be mutated also in clinical isolates with decreased susceptibility to solithromycin. While many mutations were in coding sequences, some were found in regulatory regions. These included novel phenotypic mutations in the intergenic regions of the macrolide resistance locus mef(E)/mel and in the vicinity of the ribosome binding site of erm(B). Our screens highlighted that macrolide-resistant S. pneumoniae can easily acquire resistance to solithromycin, and they revealed many new phenotypic mutations.
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Affiliation(s)
- Hélène Gingras
- Centre de Recherche en Infectiologie du Centre de Recherche du CHU de Québec and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec City, Québec, Canada
| | - Flora Peillard-Fiorente
- Centre de Recherche en Infectiologie du Centre de Recherche du CHU de Québec and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec City, Québec, Canada
| | - Chantal Godin
- Centre de Recherche en Infectiologie du Centre de Recherche du CHU de Québec and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec City, Québec, Canada
| | - Kevin Patron
- Centre de Recherche en Infectiologie du Centre de Recherche du CHU de Québec and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec City, Québec, Canada
| | - Philippe Leprohon
- Centre de Recherche en Infectiologie du Centre de Recherche du CHU de Québec and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec City, Québec, Canada
| | - Marc Ouellette
- Centre de Recherche en Infectiologie du Centre de Recherche du CHU de Québec and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec City, Québec, Canada
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Lee Y, Kim N, Roh H, Ho DT, Park J, Lee JY, Kim YJ, Kang HY, Lee J, Song JY, Kim A, Kim MS, Cho M, Choi HS, Park CI, Kim DH. Serotype distribution and antibiogram of Streptococcus parauberis isolated from fish in South Korea. Microbiol Spectr 2023; 11:e0440022. [PMID: 37555676 PMCID: PMC10581249 DOI: 10.1128/spectrum.04400-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 06/27/2023] [Indexed: 08/10/2023] Open
Abstract
Streptococcus parauberis is the dominant etiological agent of streptococcosis, the most devastating bacterial disease in the olive flounder farming industry in South Korea. In this study, the distribution of serotypes, antimicrobial susceptibility, and presence of antimicrobial resistance genes (ARGs) in S. parauberis isolates obtained between 1999 and 2021 was thoroughly investigated to gain insight into the dynamics of their presence and the relationship between serotypes and antimicrobial resistance. Disk diffusion testing of 103 isolates against 10 antimicrobial agents was performed, and epidemiological cut-off values generated through normalized resistance interpretation analysis were used to classify wild-type (WT) and non-wild-type (NWT) populations. Principal component analysis and hierarchical clustering were implemented to achieve an understanding on the relationship between serotypes and antimicrobial resistance patterns. PCR-based serotyping showed that serotype Ia (67.1%) was the most prevalent in South Korea, followed by serotypes Ib/Ic (25.2%) and II (7.7%). The highest proportion of isolates was assigned to NWT against amoxicillin (80.6%), followed by oxytetracycline (77.7%) and erythromycin (48.5%). The time-scale data showed that recently obtained serotypes Ib/Ic and II isolates tended to be categorized as NWT populations resistant to more antibiotics, possibly due to microbial adaptation to antibiotic pressure. ARGs responsible for resistance to oxytetracycline and erythromycin were found only in NWT populations in serotype Ia [tet(S) and erm(B), respectively], and serotype II [tet(M) and mef(J)-msr(I), respectively]. We also found that the mef-msr gene pair in S. parauberis serotype II might be involved in low-level resistance to erythromycin. IMPORTANCE This study presents serotype distribution and antimicrobial susceptibility data along with the antimicrobial resistance genes (ARGs) of Streptococcus parauberis, which is an important bacterial fish pathogen worldwide. In particular, almost all oxytetracycline and erythromycin non-wild-type (NWT) populations harbored tet(S) or tet(M), and erm(B) or mef(J)-msr(I), respectively. Interestingly, these ARGs were distributed in a highly serotype-dependent manner, resulting in a clear correlation between the antibiogram and serotype distribution. Moreover, recent isolates belonging to serotypes Ib/Ic and II tended to be more frequently categorized as NWT against antimicrobials, including amoxicillin and cefalexin compared to old isolates, while a dramatic decrease in erythromycin and clindamycin NWT frequencies was observed in recent serotype Ia isolates, which lacked erm(B). These variations might be attributed to shifts in the antibiotics employed in South Korean aquaculture over time. The overall findings would provide important background knowledge for understanding the epidemiology of S. parauberis infection in aquaculture.
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Affiliation(s)
- Yoonhang Lee
- Department of Aquatic Life Medicine, Pukyong National University, Busan, South Korea
| | - Nameun Kim
- Department of Aquatic Life Medicine, Pukyong National University, Busan, South Korea
| | - HeyongJin Roh
- Department of Aquatic Life Medicine, Pukyong National University, Busan, South Korea
| | - Diem Tho Ho
- Department of Aquatic Life Medicine, Pukyong National University, Busan, South Korea
| | - Jiyeon Park
- Department of Aquatic Life Medicine, Pukyong National University, Busan, South Korea
| | - Ju Yeop Lee
- Department of Aquatic Life Medicine, Pukyong National University, Busan, South Korea
| | - Yoon-Jae Kim
- Department of Aquatic Life Medicine, Pukyong National University, Busan, South Korea
| | - Hyo-Young Kang
- Department of Aquatic Life Medicine, Pukyong National University, Busan, South Korea
| | - Jungmin Lee
- Department of Aquatic Life Medicine, Pukyong National University, Busan, South Korea
| | - Jun-Young Song
- Pathology Research Division, National Institute of Fisheries Science, Busan, South Korea
| | - Ahran Kim
- Pathology Research Division, National Institute of Fisheries Science, Busan, South Korea
| | - Myoung Sug Kim
- Pathology Research Division, National Institute of Fisheries Science, Busan, South Korea
| | - Miyoung Cho
- Pathology Research Division, National Institute of Fisheries Science, Busan, South Korea
| | - Hye Sung Choi
- Pathology Research Division, National Institute of Fisheries Science, Busan, South Korea
| | - Chan-Il Park
- Department of Marine Biology and Aquaculture, Gyeongsang National University, Tongyeong, South Korea
| | - Do-Hyung Kim
- Department of Aquatic Life Medicine, Pukyong National University, Busan, South Korea
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Kong Q, Shang Z, Liu Y, Fakhar-e-Alam Kulyar M, Suo-lang S, Xu Y, Tan Z, Li J, Liu S. Preventive effect of Terminalia bellirica (Gaertn.) Roxb. extract on mice infected with Salmonella Typhimurium. Front Cell Infect Microbiol 2023; 12:1054205. [PMID: 36699727 PMCID: PMC9868565 DOI: 10.3389/fcimb.2022.1054205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 12/12/2022] [Indexed: 01/11/2023] Open
Abstract
Terminalia bellirica (Gaertn.) Roxb. (TB) is a traditional herbal combination used in Chinese medicine for the treatment of a broad range of diseases. In this study, thirty KM mice were randomly divided into control (N), infection group (NS), and the TB protection group (HS). Based on its digestive feature, intestinal physical barrier, immunological barrier and gut microbiota effects in vivo on challenged with S.typhimurium mice were investigated after oral administration of 600 mg/kg b.wt of TB for 13 days. The results show that the extract could improve the level of serum immunoglobulins (IgA and IgG), decrease the intestinal cytokine secretion to relieve intestinal cytokine storm, reinforce the intestinal biochemical barrier function by elevating the sIgA expression, and strengthen the intestinal physical barrier function. Simultaneously, based on the V3-V4 region of the 16S rRNA analyzed, the results of the taxonomic structure of the intestinal microbiota demonstrated that the TB prevention effect transformed the key phylotypes of the gut microbiota in S. Typhimurium-challenged mice and promoted the multiplication of beneficial bacteria. Furthermore, the abundance of Firmicutes and Deferribacteres increased, while that of Bacteroidetes and Actinobacteria decreased. At the genus level, the abundance of Ruminococcus and Oscillospira was substantially enhanced, while the other dominant genera showed no significant change between the vehicle control groups and the TB prevention groups. In summary, these results provide evidence that the administration of TB extract can prevent S. Typhimurium infection by alleviating the intestinal physical and immunological barriers and normalizing the gut microbiota, highlighting a promising application in clinical treatment. Thus, our results provide new insights into the biological functions of TB for the preventive effect of intestinal inflammation.
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Affiliation(s)
- Qinghui Kong
- College of Animal Science, Tibet Agricultural and Animal Husbandry University, Nyingchi, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Zhenda Shang
- College of Animal Science, Tibet Agricultural and Animal Husbandry University, Nyingchi, China
- Tibetan Plateau Feed Processing Engineering Research Center, Nyingchi, China
| | - Yao Liu
- College of Animal Science, Tibet Agricultural and Animal Husbandry University, Nyingchi, China
| | | | - Sizhu Suo-lang
- College of Animal Science, Tibet Agricultural and Animal Husbandry University, Nyingchi, China
| | - Yefen Xu
- College of Animal Science, Tibet Agricultural and Animal Husbandry University, Nyingchi, China
| | - Zhankun Tan
- College of Animal Science, Tibet Agricultural and Animal Husbandry University, Nyingchi, China
- Tibetan Plateau Feed Processing Engineering Research Center, Nyingchi, China
| | - Jiakui Li
- College of Animal Science, Tibet Agricultural and Animal Husbandry University, Nyingchi, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Suozhu Liu
- College of Animal Science, Tibet Agricultural and Animal Husbandry University, Nyingchi, China
- Tibetan Plateau Feed Processing Engineering Research Center, Nyingchi, China
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Li L, Ma J, Yu Z, Li M, Zhang W, Sun H. Epidemiological characteristics and antibiotic resistance mechanisms of Streptococcus pneumoniae: An updated review. Microbiol Res 2023; 266:127221. [DOI: 10.1016/j.micres.2022.127221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 09/13/2022] [Accepted: 10/03/2022] [Indexed: 11/27/2022]
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Use of Oral Tetracyclines in the Treatment of Adult Patients with Community-Acquired Bacterial Pneumonia: A Literature Review on the Often-Overlooked Antibiotic Class. Antibiotics (Basel) 2020; 9:antibiotics9120905. [PMID: 33327437 PMCID: PMC7764829 DOI: 10.3390/antibiotics9120905] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 12/08/2020] [Accepted: 12/11/2020] [Indexed: 12/03/2022] Open
Abstract
Oral tetracyclines have been used in clinical practice for over 60 years. Overall, one of the most common indications for use of oral tetracyclines is for treatment of adult outpatients with lower respiratory tract infections, including community-acquired pneumonia (CAP). Despite the longstanding use of oral tetracyclines, practice patterns indicate that they are often considered after other guideline-concordant oral CAP treatment options (namely macrolides, fluoroquinolones, and β-lactams). However, there are growing resistance or safety concerns with the available oral agents listed for outpatients with CAP in the updated American Thoracic Society (ATS)/Infectious Diseases Society of America (IDSA) CAP guidelines, especially among patients with comorbidities or notable risk factors for resistant pathogens. Given the need for alternative oral agents to macrolides, fluoroquinolones, and beta-lactams for adult outpatients with CAP, this review summarizes the literature on the use of oral tetracyclines (i.e., doxycycline, minocycline, and omadacycline) for this indication. As part of this review, we described their mechanism of action, common mechanisms of resistance, susceptibility profiles against common CAP pathogens, pharmacokinetics, pharmacodynamics, clinical data, and safety. The intent of the review is to highlight the important considerations when deciding between doxycycline, minocycline, and omadacycline for an adult outpatient with CAP in situations in which use of an oral tetracycline is warranted.
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Beheshti M, Jabalameli F, Feizabadi MM, Hahsemi FB, Beigverdi R, Emaneini M. Molecular characterization, antibiotic resistance pattern and capsular types of invasive Streptococcus pneumoniae isolated from clinical samples in Tehran, Iran. BMC Microbiol 2020; 20:167. [PMID: 32546124 PMCID: PMC7298763 DOI: 10.1186/s12866-020-01855-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 06/12/2020] [Indexed: 11/18/2022] Open
Abstract
Background Streptococcus pneumoniae causes serious infections worldwide. The aim of this study was to determine the molecular characteristic, antibiotic resistance pattern and capsular types of invasive S. pneumoniae in Tehran, Iran. Results Of the 44 pneumococcal invasive isolates, 39 (89%) were isolated from children and 5 (11%) from adults. The results show that all pneumococcal isolates were susceptible to linezolid but had varying resistance to trimethoprim-sulfamethoxazole (86%), erythromycin (73%), tetracycline (66%), clindamycin (43%), penicillin (16%), chloramphenicol (14%) and levofloxacin (2%). The range of erythromycin, tetracycline and penicillin MICs were 2 - ≥ 256 μg/mL, 4 - ≥ 48 μg/mL, and 0.047 - ≥ 256 respectively. All of the penicillin resistant isolates were multidrug resistant (MDR) and in addition to penicillin were resistant to tetracycline, erythromycin and trimethoprim-sulfamethoxazole. The most common capsular types detected in 64% of the pneumococcal isolates was 6A/B, 19A, 15A, 23F. The multilocus sequence typing (MLST) of 10 pneumococcal isolates revealed 9 different sequence types (STs), including ST 15139 (capsular type 19A) and ST 15140 (capsular type 23F), which have not previously been reported. Conclusions The study revealed that the S. pneumoniae isolates belonged to diverse capsular types and clones with high rate of resistance to erythromycin, tetracycline, and penicillin.
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Affiliation(s)
- Maryam Beheshti
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Building No. 7, 100 Poursina St., Keshavarz Blvd, Tehran, 14167-53955, Iran
| | - Fereshteh Jabalameli
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Building No. 7, 100 Poursina St., Keshavarz Blvd, Tehran, 14167-53955, Iran
| | - Mohammad Mehdi Feizabadi
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Building No. 7, 100 Poursina St., Keshavarz Blvd, Tehran, 14167-53955, Iran
| | - Farhad Bonakdar Hahsemi
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Building No. 7, 100 Poursina St., Keshavarz Blvd, Tehran, 14167-53955, Iran
| | - Reza Beigverdi
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Building No. 7, 100 Poursina St., Keshavarz Blvd, Tehran, 14167-53955, Iran
| | - Mohammad Emaneini
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Building No. 7, 100 Poursina St., Keshavarz Blvd, Tehran, 14167-53955, Iran.
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Yang Y, Xing S, Li S, Niu Y, Li C, Huang T, Liao X. Potential regulation of small RNAs on bacterial function activities in pig farm wastewater treatment plants. J Environ Sci (China) 2020; 91:292-300. [PMID: 32172978 DOI: 10.1016/j.jes.2020.02.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 02/01/2020] [Accepted: 02/11/2020] [Indexed: 06/10/2023]
Abstract
Small RNAs (sRNAs) are key players in the regulation of bacterial gene expression. However, the distribution and regulatory functions of sRNA in pig farm wastewater treatment plants (WWTPs) remains unknown. In this study, the wastewaters in anoxic and oxic tanks of the WWTPs were collected. The profiles of the community structure, mRNA expression, and sRNA expression of bacteria in pig farm wastewater were investigated using transcriptome sequencing and qPCR. This study demonstrated that there was a higher abundance of sRNA in the pig farm WWTPs and 52 sRNAs were detected. The sRNAs were mainly present in Proteobacteria and Firmicutes, including the potential human pathogenic bacteria (HPB) (Escherichia, Shigella, Bordetella and Morganella), crop pathogen (Pectobacterium) and denitrifying bacteria (Zobellella). And the sRNAs were involved in the bacterial functional activities such as translation, transcription, drug resistance, membrane transport and amino acid metabolism. In addition, most sRNAs had a higher abundance in anoxic tanks which contained a higher abundance of the genes associated with infectious diseases and drug resistance than that in oxic tanks. The results presented here show that in pig farm WWTPs, sRNA played an important role in bacterial function activities, especially the infectious diseases, drug resistance and denitrification, which can provide a new point of penetration for improving the pig farm WWTPs.
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Affiliation(s)
- Yiwen Yang
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Sicheng Xing
- Key Laboratory of Tropical Agricultural Environment, Ministry of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Sumin Li
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Yajing Niu
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Cheng Li
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Tuoxin Huang
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Xindi Liao
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Key Laboratory of Tropical Agricultural Environment, Ministry of Agriculture, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, South China Agriculture University, Guangzhou 510642, China.
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Sun T, Li XD, Hong J, Liu C, Zhang XL, Zheng JP, Xu YJ, Ou ZY, Zheng JL, Yu DJ. Inhibitory Effect of Two Traditional Chinese Medicine Monomers, Berberine and Matrine, on the Quorum Sensing System of Antimicrobial-Resistant Escherichia coli. Front Microbiol 2019; 10:2584. [PMID: 31798551 PMCID: PMC6863804 DOI: 10.3389/fmicb.2019.02584] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 10/24/2019] [Indexed: 01/05/2023] Open
Abstract
The quorum sensing (QS) system controls bacterial biofilm formation, which is highly related to the virulence and resistance of pathogens. In the present study, the effect of two traditional Chinese medicine (TCM) monomers, berberine and matrine, on biofilm formation and QS-related gene expression of antimicrobial-resistant (AMR) Escherichia coli strains was investigated by laser scanning confocal microscopy (LSCM) observation and real-time PCR. The results indicated a roughly positive relationship between biofilm formation ability and antimicrobial resistance. LSCM observation showed that berberine and matrine inhibited biofilm formation of AMR E. coli strains at 1/2 minimal inhibitory concentration (MIC) (1/2 MIC berberine at OD630: 0.1020; 1/2 MIC matrine: OD630: 0.1045); furthermore, abnormal cell morphology such as rounded and elongated cells was also observed. This finding was consistent with the downregulation of QS-related genes: luxS, pfS, sdiA, hflX, motA, and fliA. At 1/2 MIC and 1/4 MIC concentrations of berberine, a significant downregulation of luxS, pfS, hflX, ftsQ, and ftsE was observed. The results indicate that berberine and matrine can inhibit biofilm formation by inhibiting the QS system and that berberine is more effective than matrine.
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Affiliation(s)
- Tong Sun
- Fujian Key Laboratory of Traditional Chinese Veterinary Medicine and Animal Health, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiao-Dong Li
- Fujian Key Laboratory of Traditional Chinese Veterinary Medicine and Animal Health, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Juan Hong
- Fujian Key Laboratory of Traditional Chinese Veterinary Medicine and Animal Health, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Can Liu
- Fujian Key Laboratory of Traditional Chinese Veterinary Medicine and Animal Health, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xin-Luo Zhang
- Fujian Key Laboratory of Traditional Chinese Veterinary Medicine and Animal Health, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jin-Ping Zheng
- Fujian Key Laboratory of Traditional Chinese Veterinary Medicine and Animal Health, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuan-Jun Xu
- Fujian Key Laboratory of Traditional Chinese Veterinary Medicine and Animal Health, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zheng-Yang Ou
- Fujian Key Laboratory of Traditional Chinese Veterinary Medicine and Animal Health, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jing-Ling Zheng
- Fujian Key Laboratory of Traditional Chinese Veterinary Medicine and Animal Health, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Dao-Jin Yu
- Fujian Key Laboratory of Traditional Chinese Veterinary Medicine and Animal Health, Fujian Agriculture and Forestry University, Fuzhou, China
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10
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Multidrug ABC transporters in bacteria. Res Microbiol 2019; 170:381-391. [DOI: 10.1016/j.resmic.2019.06.001] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Revised: 06/12/2019] [Accepted: 06/17/2019] [Indexed: 12/23/2022]
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11
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Gain- and Loss-of-Function Screens Coupled to Next-Generation Sequencing for Antibiotic Mode of Action and Resistance Studies in Streptococcus pneumoniae. Antimicrob Agents Chemother 2019; 63:AAC.02381-18. [PMID: 30783004 DOI: 10.1128/aac.02381-18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 02/08/2019] [Indexed: 12/23/2022] Open
Abstract
Two whole-genome screening approaches are described for studying the mode of action and the mechanisms of resistance to trimethoprim (TMP) in the Gram-positive Streptococcus pneumoniae The gain-of-function approach (Int-Seq) relies on a genomic library of DNA fragments integrated into a fucose-inducible cassette. The second approach, leading to both gain- and loss-of-function mutation, is based on chemical mutagenesis coupled to next-generation sequencing (Mut-Seq). Both approaches pointed at the drug target dihydrofolate reductase (DHFR) as a major resistance mechanism to TMP. Resistance was achieved by dhfr overexpression either through the addition of fucose (Int-Seq) or by mutations upstream of the gene (Mut-Seq). Three types of mutations increased expression by disrupting a predicted Rho-independent terminator upstream of dhfr Known and novel DHFR mutations were also detected by Mut-Seq, and these were functionally validated for TMP resistance. The two approaches also suggested that an increase in the metabolic flux from purine synthesis to GTP and then to folate can modulate the susceptibility to TMP. Finally, we provide evidence for a novel role of the ABC transporter PatAB in TMP susceptibility. Our genomic screens highlighted novel aspects on the mode of action and mechanisms of resistance to antibiotics.
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12
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Antimicrobial susceptibility of bifidobacteria from probiotic milk products and determination of the genetic basis of tetracycline resistance in Enterococcus species after in vitro conjugation with Bifidobacterium animalis subsp. lactis. Food Control 2018. [DOI: 10.1016/j.foodcont.2018.07.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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13
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Gingras H, Dridi B, Leprohon P, Ouellette M. Coupling next-generation sequencing to dominant positive screens for finding antibiotic cellular targets and resistance mechanisms in Escherichia coli. Microb Genom 2018; 4. [PMID: 29319470 PMCID: PMC5857375 DOI: 10.1099/mgen.0.000148] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
In order to expedite the discovery of genes coding for either drug targets or antibiotic resistance, we have developed a functional genomic strategy termed Plas-Seq. This technique involves coupling a multicopy suppressor library to next-generation sequencing. We generated an Escherichia coli plasmid genomic library that was transformed into E. coli. These transformants were selected step by step using 0.25× to 2× minimum inhibitory concentrations for ceftriaxone, gentamicin, levofloxacin, tetracycline or trimethoprim. Plasmids were isolated at each selection step and subjected to Illumina sequencing. By searching for genomic loci whose sequencing coverage increased with antibiotic pressure we were able to detect 48 different genomic loci that were enriched by at least one antibiotic. Fifteen of these loci were studied functionally, and we showed that 13 can decrease the susceptibility of E. coli to antibiotics when overexpressed. These genes coded for drug targets, transcription factors, membrane proteins and resistance factors. The technique of Plas-Seq is expediting the discovery of genes associated with the mode of action or resistance to antibiotics and led to the isolation of a novel gene influencing drug susceptibility. It has the potential for being applied to novel molecules and to other microbial species.
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Affiliation(s)
- Hélène Gingras
- Centre de Recherche en Infectiologie, Université Laval, Québec, Canada
| | - Bédis Dridi
- Centre de Recherche en Infectiologie, Université Laval, Québec, Canada
| | - Philippe Leprohon
- Centre de Recherche en Infectiologie, Université Laval, Québec, Canada
| | - Marc Ouellette
- Centre de Recherche en Infectiologie, Université Laval, Québec, Canada
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14
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El Khoury JY, Boucher N, Bergeron MG, Leprohon P, Ouellette M. Penicillin induces alterations in glutamine metabolism in Streptococcus pneumoniae. Sci Rep 2017; 7:14587. [PMID: 29109543 PMCID: PMC5673960 DOI: 10.1038/s41598-017-15035-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 10/19/2017] [Indexed: 11/09/2022] Open
Abstract
Penicillin is a bactericidal antibiotic that inhibits the synthesis of the peptidoglycan by targeting penicillin-binding proteins. This study aimed to assess through transcriptional profiling the stress response of S. pneumoniae strains after exposure to lethal penicillin concentrations to understand further the mode of action of penicillin. Two experimental designs (time-course and dose-response) were used for monitoring the effect of penicillin on the transcriptional profile. The expression of some genes previously shown to be modulated by penicillin was altered, including ciaRH, pstS and clpL. Genes of the glnRA and glnPQ operons were among the most downregulated genes in the three strains. These genes are involved in glutamine synthesis and uptake and LC-MS work confirmed that penicillin treatment increases the intracellular glutamine concentrations. Glutamine conferred a protective role against penicillin when added to the culture medium. Glutamine synthetase encoded by glnA catalyses the transformation of glutamate and ammonium into glutamine and its chemical inhibition by the inhibitor L-methionine sulfoximine is shown to sensitize S. pneumoniae to penicillin, including penicillin-resistant clinical isolates. In summary, a combination of RNA-seq and metabolomics revealed that penicillin interferes with glutamine metabolism suggesting strategies that could eventually be exploited for combination therapy or for reversal of resistance.
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Affiliation(s)
- Jessica Y El Khoury
- Centre de Recherche en Infectiologie du Centre de Recherche du CHU de Québec and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec, Québec, Canada
| | - Nancy Boucher
- Centre de Recherche en Infectiologie du Centre de Recherche du CHU de Québec and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec, Québec, Canada
| | - Michel G Bergeron
- Centre de Recherche en Infectiologie du Centre de Recherche du CHU de Québec and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec, Québec, Canada
| | - Philippe Leprohon
- Centre de Recherche en Infectiologie du Centre de Recherche du CHU de Québec and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec, Québec, Canada
| | - Marc Ouellette
- Centre de Recherche en Infectiologie du Centre de Recherche du CHU de Québec and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec, Québec, Canada.
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15
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El Moujaber G, Osman M, Rafei R, Dabboussi F, Hamze M. Molecular mechanisms and epidemiology of resistance in Streptococcus pneumoniae in the Middle East region. J Med Microbiol 2017. [DOI: 10.1099/jmm.0.000503] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Grace El Moujaber
- Laboratoire Microbiologie Santé et Environnement (LMSE), Ecole Doctorale des Sciences et de Technologie, Faculté de Santé Publique, Université Libanaise, Tripoli, Lebanon
| | - Marwan Osman
- Laboratoire Microbiologie Santé et Environnement (LMSE), Ecole Doctorale des Sciences et de Technologie, Faculté de Santé Publique, Université Libanaise, Tripoli, Lebanon
| | - Rayane Rafei
- Laboratoire Microbiologie Santé et Environnement (LMSE), Ecole Doctorale des Sciences et de Technologie, Faculté de Santé Publique, Université Libanaise, Tripoli, Lebanon
| | - Fouad Dabboussi
- Laboratoire Microbiologie Santé et Environnement (LMSE), Ecole Doctorale des Sciences et de Technologie, Faculté de Santé Publique, Université Libanaise, Tripoli, Lebanon
| | - Monzer Hamze
- Laboratoire Microbiologie Santé et Environnement (LMSE), Ecole Doctorale des Sciences et de Technologie, Faculté de Santé Publique, Université Libanaise, Tripoli, Lebanon
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16
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Ellington MJ, Ekelund O, Aarestrup FM, Canton R, Doumith M, Giske C, Grundman H, Hasman H, Holden MTG, Hopkins KL, Iredell J, Kahlmeter G, Köser CU, MacGowan A, Mevius D, Mulvey M, Naas T, Peto T, Rolain JM, Samuelsen Ø, Woodford N. The role of whole genome sequencing in antimicrobial susceptibility testing of bacteria: report from the EUCAST Subcommittee. Clin Microbiol Infect 2016; 23:2-22. [PMID: 27890457 DOI: 10.1016/j.cmi.2016.11.012] [Citation(s) in RCA: 317] [Impact Index Per Article: 39.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 11/18/2016] [Indexed: 12/11/2022]
Abstract
Whole genome sequencing (WGS) offers the potential to predict antimicrobial susceptibility from a single assay. The European Committee on Antimicrobial Susceptibility Testing established a subcommittee to review the current development status of WGS for bacterial antimicrobial susceptibility testing (AST). The published evidence for using WGS as a tool to infer antimicrobial susceptibility accurately is currently either poor or non-existent and the evidence / knowledge base requires significant expansion. The primary comparators for assessing genotypic-phenotypic concordance from WGS data should be changed to epidemiological cut-off values in order to improve differentiation of wild-type from non-wild-type isolates (harbouring an acquired resistance). Clinical breakpoints should be a secondary comparator. This assessment will reveal whether genetic predictions could also be used to guide clinical decision making. Internationally agreed principles and quality control (QC) metrics will facilitate early harmonization of analytical approaches and interpretive criteria for WGS-based predictive AST. Only data sets that pass agreed QC metrics should be used in AST predictions. Minimum performance standards should exist and comparative accuracies across different WGS laboratories and processes should be measured. To facilitate comparisons, a single public database of all known resistance loci should be established, regularly updated and strictly curated using minimum standards for the inclusion of resistance loci. For most bacterial species the major limitations to widespread adoption for WGS-based AST in clinical laboratories remain the current high-cost and limited speed of inferring antimicrobial susceptibility from WGS data as well as the dependency on previous culture because analysis directly on specimens remains challenging. For most bacterial species there is currently insufficient evidence to support the use of WGS-inferred AST to guide clinical decision making. WGS-AST should be a funding priority if it is to become a rival to phenotypic AST. This report will be updated as the available evidence increases.
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Affiliation(s)
- M J Ellington
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, London, UK
| | - O Ekelund
- Department of Clinical Microbiology and the EUCAST Development Laboratory, Kronoberg Region, Central Hospital, Växjö, Sweden
| | - F M Aarestrup
- National Food Institute, Research Group for Genomic Epidemiology, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - R Canton
- Servicio de Microbiología, Hospital Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
| | - M Doumith
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, London, UK
| | - C Giske
- Department of Laboratory Medicine, Karolinska Institute and Karolinska University Hospital, Stockholm, Sweden
| | - H Grundman
- University Medical Centre Freiburg, Infection Prevention and Hospital Hygiene, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - H Hasman
- Statens Serum Institute, Department of Microbiology and Infection Control, Copenhagen, Denmark
| | - M T G Holden
- School of Medicine, Medical & Biological Sciences, North Haugh, University of St Andrews, UK
| | - K L Hopkins
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, London, UK
| | - J Iredell
- Westmead Institute for Medical Research, University of Sydney and Marie Bashir Institute, Sydney, NSW, Australia
| | - G Kahlmeter
- Department of Clinical Microbiology and the EUCAST Development Laboratory, Kronoberg Region, Central Hospital, Växjö, Sweden
| | - C U Köser
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - A MacGowan
- Department of Medical Microbiology, North Bristol NHS Trust, Southmead Hospital, Bristol, UK
| | - D Mevius
- Central Veterinary Institute (CVI) part of Wageningen University and Research Centre (WUR), Lelystad, The Netherlands; Department of Infectious Diseases and Immunology, Utrecht University, Utrecht, The Netherlands
| | - M Mulvey
- National Microbiology Laboratory, Winnipeg, Manitoba, Canada
| | - T Naas
- French National Reference Centre for Antibiotic Resistance, Bacteriology-Hygiene unit, Hôpital Bicêtre, APHP, LabEx LERMIT, University Paris Sud, Le Kremlin-Bicêtre, France
| | - T Peto
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - J-M Rolain
- PU-PH des Disciplines Pharmaceutiques, 1-URMITE CNRS IRD UMR 6236, IHU Méditerranée Infection, Valorization and Transfer, Aix Marseille Université, Faculté de Médecine et de Pharmacie, Marseille, France
| | - Ø Samuelsen
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, University Hospital of North Norway, Department of Microbiology and Infection Control, Tromsø, Norway
| | - N Woodford
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, London, UK.
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17
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Ceyssens PJ, Van Bambeke F, Mattheus W, Bertrand S, Fux F, Van Bossuyt E, Damée S, Nyssen HJ, De Craeye S, Verhaegen J, Tulkens PM, Vanhoof R. Molecular Analysis of Rising Fluoroquinolone Resistance in Belgian Non-Invasive Streptococcus pneumoniae Isolates (1995-2014). PLoS One 2016; 11:e0154816. [PMID: 27227336 PMCID: PMC4881901 DOI: 10.1371/journal.pone.0154816] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 04/19/2016] [Indexed: 11/25/2022] Open
Abstract
We present the results of a longitudinal surveillance study (1995–2014) on fluoroquinolone resistance (FQ-R) among Belgian non-invasive Streptococcus pneumoniae isolates (n = 5,602). For many years, the switch to respiratory fluoroquinolones for the treatment of (a)typical pneumonia had no impact on FQ-R levels. However, since 2011 we observed a significant decrease in susceptibility towards ciprofloxacin, ofloxacin and levofloxacin with peaks of 9.0%, 6.6% and 3.1% resistant isolates, respectively. Resistance to moxifloxacin arised sporadically, and remained <1% throughout the entire study period. We observed classical topoisomerase mutations in gyrA (n = 25), parC (n = 46) and parE (n = 3) in varying combinations, arguing against clonal expansion of FQ-R. The impact of recombination with co-habiting commensal streptococci on FQ-R remains marginal (10.4%). Notably, we observed that a rare combination of DNA Gyrase mutations (GyrA_S81L/GyrB_P454S) suffices for high-level moxifloxacin resistance, contrasting current model. Interestingly, 85/422 pneumococcal strains display MICCIP values which were lowered by at least four dilutions by reserpine, pointing at involvement of efflux pumps in FQ-R. In contrast to susceptible strains, isolates resistant to ciprofloxacin significantly overexpressed the ABC pump PatAB in comparison to reference strain S. pneumoniae ATCC 49619, but this could only be linked to disruptive terminator mutations in a fraction of these. Conversely, no difference in expression of the Major Facilitator PmrA, unaffected by reserpine, was noted between susceptible and resistant S. pneumoniae strains. Finally, we observed that four isolates displayed intermediate to high-level ciprofloxacin resistance without any known molecular resistance mechanism. Focusing future molecular studies on these isolates, which are also commonly found in other studies, might greatly assist in the battle against rising pneumococcal drug resistance.
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Affiliation(s)
- Pieter-Jan Ceyssens
- Unit of Bacterial Diseases, Scientific Institute of Public Health (WIV-ISP), 1050 Brussels, Belgium
| | - Françoise Van Bambeke
- Pharmacologie cellulaire et moléculaire, Louvain Drug Research Institute, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Wesley Mattheus
- Unit of Bacterial Diseases, Scientific Institute of Public Health (WIV-ISP), 1050 Brussels, Belgium
| | - Sophie Bertrand
- Unit of Bacterial Diseases, Scientific Institute of Public Health (WIV-ISP), 1050 Brussels, Belgium
| | - Frédéric Fux
- Unit of Bacterial Diseases, Scientific Institute of Public Health (WIV-ISP), 1050 Brussels, Belgium
| | - Eddie Van Bossuyt
- Unit of Bacterial Diseases, Scientific Institute of Public Health (WIV-ISP), 1050 Brussels, Belgium
| | - Sabrina Damée
- Unit of Bacterial Diseases, Scientific Institute of Public Health (WIV-ISP), 1050 Brussels, Belgium
| | - Henry-Jean Nyssen
- Unit of Foodborne Pathogens, Scientific Institute of Public Health (WIV-ISP), 1050 Brussels, Belgium
| | - Stéphane De Craeye
- Unit of Foodborne Pathogens, Scientific Institute of Public Health (WIV-ISP), 1050 Brussels, Belgium
| | - Jan Verhaegen
- Laboratory of Clinical Bacteriology and Mycology, KULeuven, 3000 Leuven, Belgium
| | | | - Paul M. Tulkens
- Pharmacologie cellulaire et moléculaire, Louvain Drug Research Institute, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Raymond Vanhoof
- Unit of Bacterial Diseases, Scientific Institute of Public Health (WIV-ISP), 1050 Brussels, Belgium
- * E-mail:
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18
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Leprohon P, Gingras H, Ouennane S, Moineau S, Ouellette M. A genomic approach to understand interactions between Streptococcus pneumoniae and its bacteriophages. BMC Genomics 2015; 16:972. [PMID: 26582495 PMCID: PMC4652380 DOI: 10.1186/s12864-015-2134-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 10/23/2015] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Bacteriophage replication depends on bacterial proteins and inactivation of genes coding for such host factors should interfere with phage infection. To gain further insights into the interactions between S. pneumoniae and its pneumophages, we characterized S. pneumoniae mutants selected for resistance to the virulent phages SOCP or Dp-1. RESULTS S. pneumoniae R6-SOCP(R) and R6-DP1(R) were highly resistant to the phage used for their selection and no cross-resistance between the two phages was detected. Adsorption of SOCP to R6-SOCP(R) was partly reduced whereas no difference in Dp-1 adsorption was noted on R6-DP1(R). The replication of SOCP was completely inhibited in R6-SOCP(R) while Dp-1 was severely impaired in R6-DP1(R). Genome sequencing identified 8 and 2 genes mutated in R6-SOCP(R) and R6-DP1(R), respectively. Resistance reconstruction in phage-sensitive S. pneumoniae confirmed that mutations in a GntR-type regulator, in a glycerophosphoryl phosphodiesterase and in a Mur ligase were responsible for resistance to SOCP. The three mutations were additive to increase resistance to SOCP. In contrast, resistance to Dp-1 in R6-DP1(R) resulted from mutations in a unique gene coding for a type IV restriction endonuclease. CONCLUSION The characterization of mutations conferring resistance to pneumophages highlighted that diverse host genes are involved in the replication of phages from different families.
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Affiliation(s)
- Philippe Leprohon
- Centre de recherche en Infectiologie du Centre de Recherche du CHU de Québec, Université Laval, 2705 Boul. Laurier, Québec, QC, Canada, , G1V 4G2. .,Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, 1050, avenue de la Médecine, Québec, QC, Canada, , G1V 0A6.
| | - Hélène Gingras
- Centre de recherche en Infectiologie du Centre de Recherche du CHU de Québec, Université Laval, 2705 Boul. Laurier, Québec, QC, Canada, , G1V 4G2. .,Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, 1050, avenue de la Médecine, Québec, QC, Canada, , G1V 0A6.
| | - Siham Ouennane
- Département de Biochimie, Microbiologie et Bio-informatique and PROTEO, Faculté des Sciences et Génie, Université Laval, Québec, QC, Canada. .,Félix d'Hérelle Reference Center for Bacterial Viruses and GREB, Faculté de Médecine Dentaire, Université Laval, Québec, QC, Canada.
| | - Sylvain Moineau
- Département de Biochimie, Microbiologie et Bio-informatique and PROTEO, Faculté des Sciences et Génie, Université Laval, Québec, QC, Canada. .,Félix d'Hérelle Reference Center for Bacterial Viruses and GREB, Faculté de Médecine Dentaire, Université Laval, Québec, QC, Canada.
| | - Marc Ouellette
- Centre de recherche en Infectiologie du Centre de Recherche du CHU de Québec, Université Laval, 2705 Boul. Laurier, Québec, QC, Canada, , G1V 4G2. .,Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, 1050, avenue de la Médecine, Québec, QC, Canada, , G1V 0A6.
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Punina NV, Makridakis NM, Remnev MA, Topunov AF. Whole-genome sequencing targets drug-resistant bacterial infections. Hum Genomics 2015; 9:19. [PMID: 26243131 PMCID: PMC4525730 DOI: 10.1186/s40246-015-0037-z] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 07/03/2015] [Indexed: 01/07/2023] Open
Abstract
During the past two decades, the technological progress of whole-genome sequencing (WGS) had changed the fields of Environmental Microbiology and Biotechnology, and, currently, is changing the underlying principles, approaches, and fundamentals of Public Health, Epidemiology, Health Economics, and national productivity. Today’s WGS technologies are able to compete with conventional techniques in cost, speed, accuracy, and resolution for day-to-day control of infectious diseases and outbreaks in clinical laboratories and in long-term epidemiological investigations. WGS gives rise to an exciting future direction for personalized Genomic Epidemiology. One of the most vital and growing public health problems is the emerging and re-emerging of multidrug-resistant (MDR) bacterial infections in the communities and healthcare settings, reinforced by a decline in antimicrobial drug discovery. In recent years, retrospective analysis provided by WGS has had a great impact on the identification and tracking of MDR microorganisms in hospitals and communities. The obtained genomic data are also important for developing novel easy-to-use diagnostic assays for clinics, as well as for antibiotic and therapeutic development at both the personal and population levels. At present, this technology has been successfully applied as an addendum to the real-time diagnostic methods currently used in clinical laboratories. However, the significance of WGS for public health may increase if: (a) unified and user-friendly bioinformatics toolsets for easy data interpretation and management are established, and (b) standards for data validation and verification are developed. Herein, we review the current and future impact of this technology on diagnosis, prevention, treatment, and control of MDR infectious bacteria in clinics and on the global scale.
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Affiliation(s)
- N V Punina
- Bach Institute of Biochemistry, Russian Academy of Science, Moscow, 119071, Russia.
| | - N M Makridakis
- Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, 70112, USA
| | - M A Remnev
- The Federal State Unitary Enterprise All-Russia Research Institute of Automatics, Moscow, 127055, Russia
| | - A F Topunov
- Bach Institute of Biochemistry, Russian Academy of Science, Moscow, 119071, Russia
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20
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Induced tigecycline resistance inStreptococcus pneumoniaemutants reveals mutations in ribosomal proteins and rRNA. J Antimicrob Chemother 2015; 70:2973-80. [DOI: 10.1093/jac/dkv211] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 06/21/2015] [Indexed: 11/12/2022] Open
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