1
|
Zhang H, Tang M, Li D, Xu M, Ao Y, Lin L. Applications and advances in molecular diagnostics: revolutionizing non-tuberculous mycobacteria species and subspecies identification. Front Public Health 2024; 12:1410672. [PMID: 38962772 PMCID: PMC11220129 DOI: 10.3389/fpubh.2024.1410672] [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: 04/01/2024] [Accepted: 06/10/2024] [Indexed: 07/05/2024] Open
Abstract
Non-tuberculous mycobacteria (NTM) infections pose a significant public health challenge worldwide, affecting individuals across a wide spectrum of immune statuses. Recent epidemiological studies indicate rising incidence rates in both immunocompromised and immunocompetent populations, underscoring the need for enhanced diagnostic and therapeutic approaches. NTM infections often present with symptoms similar to those of tuberculosis, yet with less specificity, increasing the risk of misdiagnosis and potentially adverse outcomes for patients. Consequently, rapid and accurate identification of the pathogen is crucial for precise diagnosis and treatment. Traditional detection methods, notably microbiological culture, are hampered by lengthy incubation periods and a limited capacity to differentiate closely related NTM subtypes, thereby delaying diagnosis and the initiation of targeted therapies. Emerging diagnostic technologies offer new possibilities for the swift detection and accurate identification of NTM infections, playing a critical role in early diagnosis and providing more accurate and comprehensive information. This review delineates the current molecular methodologies for NTM species and subspecies identification. We critically assess the limitations and challenges inherent in these technologies for diagnosing NTM and explore potential future directions for their advancement. It aims to provide valuable insights into advancing the application of molecular diagnostic techniques in NTM infection identification.
Collapse
Affiliation(s)
- Haiyang Zhang
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
| | - Maoting Tang
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
| | - Deyuan Li
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
| | - Min Xu
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
| | - Yusen Ao
- Department of Pediatrics, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Liangkang Lin
- Department of Pediatrics, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| |
Collapse
|
2
|
Abbas M, Khan MT, Iqbal Z, Ali A, Eddine BT, Yousaf N, Wei D. Sources, transmission and hospital-associated outbreaks of nontuberculous mycobacteria: a review. Future Microbiol 2024; 19:715-740. [PMID: 39015998 PMCID: PMC11259073 DOI: 10.2217/fmb-2023-0279] [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: 12/14/2023] [Accepted: 03/20/2024] [Indexed: 07/18/2024] Open
Abstract
Nontuberculous mycobacteria (NTM) are widespread environmental organisms found in both natural and man-made settings, such as building plumbing, water distribution networks and hospital water systems. Their ubiquitous presence increases the risk of transmission, leading to a wide range of human infections, particularly in immunocompromised individuals. NTM primarily spreads through environmental exposures, such as inhaling aerosolized particles, ingesting contaminated food and introducing it into wounds. Hospital-associated outbreaks have been linked to contaminated medical devices and water systems. Furthermore, the rising global incidence, prevalence and isolation rates highlight the urgency of addressing NTM infections. Gaining a thorough insight into the sources and epidemiology of NTM infection is crucial for devising novel strategies to prevent and manage NTM transmission and infections.
Collapse
Affiliation(s)
- Munawar Abbas
- College of Food Science & Technology, Henan University of Technology, Zhengzhou, Henan, 450001, China
| | - Muhammad Tahir Khan
- Institute of Molecular Biology & Biotechnology (IMBB), The University of Lahore, 1KM Defense Road, Lahore, 58810, Pakistan
- Zhongjing Research & Industrialization Institute of Chinese Medicine, Zhongguancun Scientific Park, Meixi, Nanyang, Henan, 473006, PR China
| | - Zafar Iqbal
- School of Life Science, Anhui Normal University, Wuhu, Anhui, China
| | - Arif Ali
- Department of Bioinformatics & Biological Statistics, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Benarfa Taki Eddine
- Echahid Cheikh Larbi Tebessi University Faculty of Exact Sciences & Natural & Life Sciences, Département of Microbiology, Algeria
| | - Numan Yousaf
- Department of Biosciences, COMSATS University Islamabad, Pakistan
| | - Dongqing Wei
- College of Food Science & Technology, Henan University of Technology, Zhengzhou, Henan, 450001, China
- State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint International Research Laboratory of Metabolic & Developmental Sciences & School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, PR China
- Zhongjing Research & Industrialization Institute of Chinese Medicine, Zhongguancun Scientific Park, Meixi, Nanyang, Henan, 473006, PR China
- Henan Biological Industry Group, 41, Nongye East Rd, Jinshui, Zhengzhou, Henan, 450008, China
- Peng Cheng National Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nashan District, Shenzhen, Guangdong, 518055, PR China
| |
Collapse
|
3
|
Kim YJ, Kim S, Ham H, Yu S, Choo HJ, Kim HJ, Heo R, Choi G, Kim SH, Lee HJ. Trend of nontuberculous mycobacteria species and minimal inhibitory concentration in a referral laboratory in Korea from 2013 to 2019. J Infect Public Health 2024; 17:212-216. [PMID: 38113818 DOI: 10.1016/j.jiph.2023.11.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 11/06/2023] [Accepted: 11/30/2023] [Indexed: 12/21/2023] Open
Abstract
BACKGROUND This study investigated the trends of nontuberculous mycobacterial (NTM) isolates and the minimal inhibitory concentrations (MIC) of antimicrobial agents in Korea. METHODS Data from 2013 to 2019 were collected from 69 medical institutions through 12 branches of the Korean Institute of Tuberculosis. NTM identification was conducted using the Advansure Mycobacteria Genoblot assay. The MIC of antibiotics against NTM species were measured using the broth microdilution method according to the Clinical and Laboratory Standards Institute guidelines. RESULTS Over seven years, 86,194 NTM identifications were requested, with an annual increase from 8034 in 2013-17,229 in 2019. The most frequently identified NTM species were M. intracellulare (33,467; 47.3%) and M. avium (19,818; 27.2%), followed by M. abscessus (6858; 9.4%) and M. massiliense (3156; 4.3%). Regarding the antimicrobial agents, imipenem exhibited the greatest difference in MIC between M. intracellulare and M. avium, whereas clarithromycin showed the most significant difference between M. abscessus and M. massiliense. No notable changes were observed in the annual MIC distribution of most antibacterial agents, except for clarithromycin in M. abscessus. CONCLUSIONS The prevalence of NTM in Korea is gradually increasing, and follow-up studies on NTM isolates identified as the causative agents of infection are needed.
Collapse
Affiliation(s)
- Young Jin Kim
- Department of Laboratory Medicine, Kyung Hee University College of Medicine, Kyung Hee University Hospital, Seoul, Republic of Korea
| | - Seungmo Kim
- Laboratory Medicine Center, The Korean Institute of Tuberculosis, Korean National Tuberculosis Association, Cheongju, Republic of Korea
| | - Heejung Ham
- Department of Laboratory Medicine, Kyung Hee University Hospital, Seoul, Republic of Korea
| | - Sarah Yu
- College of Health Science, Korea University, Seoul, Republic of Korea
| | - Hyeon-Ju Choo
- Clinical Laboratory Center, Korean National Tuberculosis Association, Seoul, Republic of Korea
| | - Hwi-Jun Kim
- Laboratory Medicine Center, The Korean Institute of Tuberculosis, Korean National Tuberculosis Association, Cheongju, Republic of Korea
| | - Ryeun Heo
- Laboratory Medicine Center, The Korean Institute of Tuberculosis, Korean National Tuberculosis Association, Cheongju, Republic of Korea
| | - Gyeongsik Choi
- Laboratory Medicine Center, The Korean Institute of Tuberculosis, Korean National Tuberculosis Association, Cheongju, Republic of Korea
| | - Soul-Hee Kim
- Laboratory Medicine Center, The Korean Institute of Tuberculosis, Korean National Tuberculosis Association, Cheongju, Republic of Korea
| | - Hee Joo Lee
- Clinical Laboratory Center, Korean National Tuberculosis Association, Seoul, Republic of Korea.
| |
Collapse
|
4
|
Yang J, Hu Y, Zhang Y, Zhou S, Meng D, Xia S, Wang H. Deciphering the diversity and assemblage mechanisms of nontuberculous mycobacteria community in four drinking water distribution systems with different disinfectants. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 907:168176. [PMID: 37907107 DOI: 10.1016/j.scitotenv.2023.168176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 10/25/2023] [Accepted: 10/26/2023] [Indexed: 11/02/2023]
Abstract
Nontuberculous mycobacteria (NTM) represent an emerging health concern due to their escalating infections worldwide. Although drinking water distribution systems (DWDSs) have been considered as NTM reservoirs and a potential infection route, NTM community at the species level remain largely elusive in DWDSs. This study employed high-throughput sequencing coupled with qPCR to profile NTM community and estimate their abundances at the species level in water and biofilm samples in four DWDSs using three different disinfectants (i.e. free chlorine, chloramine and chlorine dioxide). Results demonstrated the dominance of Mycobacterium paragordonae and Mycobacterium mucogenicum in both biofilm and water across four DWDSs, whereas Mycobacterium abscessus and Mycobacterium chelonae, the two clinically significant species, exhibited low abundance but high prevalence. Comparable NTM community was observed in biofilm across these four DWDSs. Distinct separation of NTM community between SH-chloramine DWDSs water and other DWDSs highlighted the selective pressure of chloramine on NTM community. Furthermore, the research revealed that biofilm and water exhibited distinct NTM community structures, with biofilm harboring more diverse NTM community. Certain NTM species displayed a preference for biofilm, such as Mycobacterium gordonae, while others, like Mycobacterium mucogenicum, were more abundant in water samples (P < 0.05). In terms of NTM community assembly, stochastic processes dominated biofilm, while comparable role of stochastic and deterministic processes was observed in water. In conclusion, this study offers a pioneering and comprehensive insight into the dynamics and assembly mechanisms of NTM community within four DWDSs treated with three distinct disinfectants. These findings serve as a critical foundation for assessing NTM exposure risks and devising effective management strategies within DWDSs.
Collapse
Affiliation(s)
- Jinhao Yang
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
| | - Yuxing Hu
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
| | - Yue Zhang
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
| | - Shuang Zhou
- School of Medicine, Tongji University, Shanghai 200092, China
| | - Die Meng
- Shanghai Pulmonary Hospital, Tongji University, Shanghai 200433, China
| | - Siqing Xia
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Hong Wang
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China.
| |
Collapse
|
5
|
Baird T, Bell S. Cystic Fibrosis-Related Nontuberculous Mycobacterial Pulmonary Disease. Clin Chest Med 2023; 44:847-860. [PMID: 37890921 DOI: 10.1016/j.ccm.2023.06.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/29/2023]
Abstract
Non-tuberculous mycobacteria (NTM) infection is a major cause of morbidity in people with cystic fibrosis (pwCF) with rates of infection increasing worldwide. Accurate diagnosis and decisions surrounding best management remain challenging. Treatment guidelines have been developed to assist physicians in managing NTM in pwCF, but involve prolonged and complex mycobacterial regimens, often associated with significant toxicity. Fortunately, current management and outcomes of NTM in CF are likely to evolve due to improved understanding of disease acquisition, better diagnostics, emerging antimycobacterial therapies, and the widespread uptake of cystic fibrosis transmembrane conductance regulator (CFTR) modulator therapies.
Collapse
Affiliation(s)
- Timothy Baird
- Department of Respiratory Medicine, Sunshine Coast University Hospital, Sunshine Coast, Queensland, Australia; Sunshine Coast Health Institute, Sunshine Coast, Queensland, Australia; University of the Sunshine Coast, Sunshine Coast, Queensland, Australia.
| | - Scott Bell
- Department of Thoracic Medicine, The Prince Charles Hospital, Brisbane, Queensland, Australia; Children's Health Research Centre, Faculty of Medicine, The University of Queensland, Brisbane, Australia; Translational Research Institute, Brisbane, Queensland, Australia; Department of Thoracic Medicine, The Prince Charles Hospital, Chermside, Queensland, Australia
| |
Collapse
|
6
|
Honda JR. Environmental Sources and Transmission of Nontuberculous Mycobacteria. Clin Chest Med 2023; 44:661-674. [PMID: 37890909 DOI: 10.1016/j.ccm.2023.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/29/2023]
Abstract
The field of environmental nontuberculous mycobacteria (NTM) is benefiting from a new era of genomics that has catapulted our understanding of preferred niches, transmission, and outbreak investigations. The ability to forecast environmental features that promote or reduce environmental NTM prevalence will greatly improve with coordinated environmental sampling and by elevating the necessity for uniform disease notifications. Studies that synergize environmental biology, isolate notifications, and comparative genomics in prospective, longitudinal studies, particularly during climate changes and weather events, will be useful to solve longstanding NTM public health quandaries.
Collapse
Affiliation(s)
- Jennifer R Honda
- Department of Cellular and Molecular Biology, University of Texas Health Science Center at Tyler, 11937 US Hwy 271, BMR Building, Tyler, TX 75708, USA.
| |
Collapse
|
7
|
Reil I, Barbić L, Kompes G, Tuk MZ, Duvnjak S, Cvetnić Ž, Habrun B, Arapović J, Špičić S. Risk of zoonoses involving slow-growing non-tuberculous mycobacteria: Survey of antimicrobial resistance among strains from domestic and wild animals. J Glob Antimicrob Resist 2023; 35:6-10. [PMID: 37573944 DOI: 10.1016/j.jgar.2023.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 07/10/2023] [Accepted: 08/01/2023] [Indexed: 08/15/2023] Open
Abstract
OBJECTIVES Non-tuberculous mycobacteria are opportunistic pathogens that cause disease mainly in immunocompromised hosts. The present study assessed the prevalence of antibiotic resistance among such mycobacteria from domestic and wild animals in Croatia sampled during several years within a national surveillance program. METHODS A total of 44 isolates belonging to nine slow-growing species were genotyped and analyzed for susceptibility to 13 antimicrobials often used to treat non-tuberculous mycobacterial infections in humans. RESULTS Most prevalent resistance was to moxifloxacin (77.3%), doxycycline (76.9%), and rifampicin (76.9%), followed by ciprofloxacin (65.4%), trimethoprim-sulfamethoxazole (65.4%), and linezolid (61.4%). Few isolates were resistant to rifabutin (7.7%) or amikacin (6.8%). None of the isolates was resistant to clarithromycin. Nearly all isolates (86.4%) were resistant to multiple antibiotics. CONCLUSION Our findings suggest substantial risk that human populations may experience zoonotic infections with non-tuberculous mycobacteria that will be difficult to treat using the current generation of antibiotics. Future work should clarify how resistance emerges in wild populations of non-tuberculous mycobacteria.
Collapse
Affiliation(s)
- Irena Reil
- Croatian Veterinary Institute, Zagreb, Croatia
| | - Ljubo Barbić
- Faculty of Veterinary Medicine, University of Zagreb, Zagreb, Croatia
| | | | | | | | | | | | - Jurica Arapović
- University Clinical Hospital Mostar, Department of Infectious Diseases, Mostar, Bosnia and Herzegovina; School of Medicine, University of Mostar, Mostar, Bosnia and Herzegovina
| | | |
Collapse
|
8
|
Reil I, Špičić S, Barbić L, Duvnjak S, Kompes G, Benić M, Stojević D, Cvetnić Ž, Arapović J, Zdelar-Tuk M. Antimicrobial Resistance in Rapidly Growing Nontuberculous Mycobacteria among Domestic and Wild Animals Emphasizing the Zoonotic Potential. Microorganisms 2023; 11:2520. [PMID: 37894179 PMCID: PMC10609087 DOI: 10.3390/microorganisms11102520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 09/29/2023] [Accepted: 10/08/2023] [Indexed: 10/29/2023] Open
Abstract
Non-tuberculous mycobacteria (NTM) are opportunistic pathogens capable of causing infections in humans and animals. The aim of this study was to demonstrate the potential role of domestic and wild animals as a reservoir of multiple resistant, rapidly growing NTM strains representing a potential zoonotic threat to humans. A total of 87 animal isolates belonging to 11 rapidly growing species (visible colonies appear within three to seven days) were genotyped and tested for susceptibility to the 15 most commonly used antibiotics in the treatment of such infections in a human clinic. By determining the antimicrobial susceptibility, the most prevalent resistance was found to cephalosporins (>50%), followed by amoxicillin-clavulanate (31.0%), clarithromycin (23.0%), tobramycin (14.9%) and doxycycline (10.3%). Resistance to imipenem, ciprofloxacin, minocycline and linezolid was notably lower (<7.0%). All tested isolates were susceptible to amikacin and moxifloxacin. The most frequent resistance was proved in the most pathogenic species: M. fortuitum, M. neoaurum, M. vaccae and M. porcinum. Meanwhile, other species displayed a higher sensitivity rate. No significant resistance differences between domestic and wild animals were found. The established significant frequency of resistance highlights the significant zoonotic potential posed by circulating rapidly growing NTM strains, which could lead to challenges in the treatment of these infections.
Collapse
Affiliation(s)
- Irena Reil
- Croatian Veterinary Institute, 10000 Zagreb, Croatia; (I.R.); (S.Š.); (M.B.); (D.S.); (Ž.C.); (M.Z.-T.)
| | - Silvio Špičić
- Croatian Veterinary Institute, 10000 Zagreb, Croatia; (I.R.); (S.Š.); (M.B.); (D.S.); (Ž.C.); (M.Z.-T.)
| | - Ljubo Barbić
- The Faculty of Veterinary Medicine, University of Zagreb, 10000 Zagreb, Croatia;
| | - Sanja Duvnjak
- Croatian Veterinary Institute, 10000 Zagreb, Croatia; (I.R.); (S.Š.); (M.B.); (D.S.); (Ž.C.); (M.Z.-T.)
| | - Gordan Kompes
- Croatian Veterinary Institute, 10000 Zagreb, Croatia; (I.R.); (S.Š.); (M.B.); (D.S.); (Ž.C.); (M.Z.-T.)
| | - Miroslav Benić
- Croatian Veterinary Institute, 10000 Zagreb, Croatia; (I.R.); (S.Š.); (M.B.); (D.S.); (Ž.C.); (M.Z.-T.)
| | - Dora Stojević
- Croatian Veterinary Institute, 10000 Zagreb, Croatia; (I.R.); (S.Š.); (M.B.); (D.S.); (Ž.C.); (M.Z.-T.)
| | - Željko Cvetnić
- Croatian Veterinary Institute, 10000 Zagreb, Croatia; (I.R.); (S.Š.); (M.B.); (D.S.); (Ž.C.); (M.Z.-T.)
| | - Jurica Arapović
- Department of Infectious Diseases, University Clinical Hospital Mostar, 88000 Mostar, Bosnia and Herzegovina;
- School of Medicine, University of Mostar, 88000 Mostar, Bosnia and Herzegovina
| | - Maja Zdelar-Tuk
- Croatian Veterinary Institute, 10000 Zagreb, Croatia; (I.R.); (S.Š.); (M.B.); (D.S.); (Ž.C.); (M.Z.-T.)
| |
Collapse
|
9
|
Beinhauerova M, Slana I. Utilisation of Actiphage in combination with IS 900 qPCR as a diagnostic tool for rapid determination of paratuberculosis infection status in small ruminant herds. J Vet Res 2023; 67:347-352. [PMID: 37786842 PMCID: PMC10541669 DOI: 10.2478/jvetres-2023-0041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 07/04/2023] [Indexed: 10/04/2023] Open
Abstract
Introduction Mycobacterium avium subsp. paratuberculosis (MAP) is the causative agent of paratuberculosis, a chronic infectious intestinal disease occurring in domestic and wild ruminants. Early diagnosis of infected herds enabling timely adoption of control measures is tremendously important in view of the fact that the disease has a significant economic impact on farmers. The aim of this study was to evaluate the possibility of rapid detection of viable MAP on small ruminant farms based on environmental sample examination using a novel phage-based test named Actiphage. Material and Methods A total of 9 fresh and 28 frozen (8 or 11 years at -70°C) environmental samples originating from paratuberculosis-affected farms were analysed for the presence of MAP by four different diagnostic methods: Actiphage combined with real-time PCR targeting insertion sequence 900 (IS900 qPCR), conventional phage amplification assay, culture (frozen samples only), and direct ĪS900 qPCR. Results Viable MAP was detected in one fresh environmental sample using Actiphage-IS900 qPCR. None of the frozen samples tested positive using this diagnostic approach, which was consistent with the results of culture examination also providing information on viability. Conclusion This study describes other possible and innovative uses of phage-based methods in paratuberculosis control strategies. The Actiphage-qPCR was found to be less laborious than culture and provided results within six hours, suggesting that it may be a valuable tool for rapid initial determination of the infectious status of farmed animals based on environmental sample examination.
Collapse
Affiliation(s)
- Monika Beinhauerova
- Department of Microbiology and Antimicrobial Resistance, Veterinary Research Institute, 621 00Brno, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, 625 00Brno, Czech Republic
| | - Iva Slana
- Department of Microbiology and Antimicrobial Resistance, Veterinary Research Institute, 621 00Brno, Czech Republic
| |
Collapse
|
10
|
Song JJX, Oguma K. Mycobacterial contamination in tap and shower waters in Thailand. Lett Appl Microbiol 2023; 76:ovad090. [PMID: 37528059 DOI: 10.1093/lambio/ovad090] [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: 04/27/2023] [Revised: 07/23/2023] [Accepted: 07/31/2023] [Indexed: 08/03/2023]
Abstract
Waterborne disease is increasingly becoming associated with opportunistic premise plumbing pathogens (OPPPs), which can resist residual chlorination, regrow throughout drinking water distribution systems, and colonize premise plumbing. Nontuberculous mycobacteria (NTM) include clinically important species and exert a high burden on healthcare systems. We briefly report a qPCR-based survey of Mycobacterium spp. numbers in tap, POU-treated, and shower waters from Bangkok, Thailand. Non-stagnant tap waters and non-stagnant shower waters had mean numbers of 1.3 × 103 and 2.4 × 103 copies/mL, respectively. Water stagnation resulted in mean numbers higher by up to 1.0 log. The lowest number, 25 copies/mL, was obtained from a POU-treated sample, while the highest number, 2.0 × 104 copies/mL, came from a stagnant tap. Comparing with international data, mean numbers in this study were greater than those in nine out of 11 (82%) comparable studies, and the maximum numbers in this study were also high. Our samples of Bangkok waters exhibited relatively high Mycobacterium spp. numbers, suggesting the need for appropriate POU treatment systems where NTM infection is a health concern. This survey data can be used to set inactivation performance targets in POU water disinfection system design and may also lead to quantitative microbial risk assessment (QMRA) studies.
Collapse
Affiliation(s)
- Jack Jia Xin Song
- Department of Urban Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Kumiko Oguma
- Department of Urban Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
| |
Collapse
|
11
|
Coggins JM, Obi A, Badders J, Roy K, Duncan R, Silva C. Mycobacterium abscessus Causes Highly Resistant Infection as a Breast Abscess. Cureus 2023; 15:e38450. [PMID: 37273317 PMCID: PMC10234577 DOI: 10.7759/cureus.38450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/29/2023] [Indexed: 06/06/2023] Open
Abstract
Mycobacterium abscessus is an increasing threat to public health due to its multi-drug resistance and increasing prevalence. The pathogen most commonly causes chronic respiratory infections, but it may also invade locally through the skin and soft tissue damage caused by trauma, piercings, or tattoos. A 58-year-old African American female presented with a five-month history of recurrent abscesses in the right breast. She had previously been treated with doxycycline and ceftriaxone injections at an outside clinic with minimal improvement. Following incision and drainage, cultures and susceptibilities showed M. abscessus infection with a high level of drug resistance. Due to financial barriers, the patient received a suboptimal antibiotic regimen and required multiple surgical procedures, resulting in only temporary wound healing. At the time of this report, the patient is recovering from her fourth incision and drainage, with cultures and susceptibilities pending and discussions of a total mastectomy. M. abscessus is a highly resistant bacteria capable of causing skin and soft tissue infections of the breast. Such infections may occur without an inciting event and require extensive surgical and antimicrobial management.
Collapse
Affiliation(s)
- John M Coggins
- Surgery, University of Texas Medical Branch at Galveston, Galveston, USA
| | - Ann Obi
- Surgery, University of Texas Medical Branch at Galveston, Galveston, USA
| | - Joel Badders
- Surgery, University of Texas Medical Branch at Galveston, Galveston, USA
| | - Khushali Roy
- Surgery, University of Texas Medical Branch at Galveston, Galveston, USA
| | - Rachel Duncan
- Surgery, University of Texas Medical Branch at Galveston, Galveston, USA
| | - Colleen Silva
- Surgery, University of Texas Medical Branch at Galveston, Galveston, USA
| |
Collapse
|
12
|
Burke A, Thomson RM, Wainwright CE, Bell SC. Nontuberculous Mycobacteria in Cystic Fibrosis in the Era of Cystic Fibrosis Transmembrane Regulator Modulators. Semin Respir Crit Care Med 2023; 44:287-296. [PMID: 36649736 DOI: 10.1055/s-0042-1759883] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Nontuberculous mycobacteria (NTM) are a group of mycobacteria which represent opportunistic pathogens that are of increasing concern in people with cystic fibrosis (pwCF). The acquisition has been traditionally though to be from environmental sources, though recent work has suggested clustered clonal infections do occur and transmission potential demonstrated among pwCF attending CF specialist centers. Guidelines for the screening, diagnosis, and identification of NTM and management of pwCF have been published. The emergence of CF-specific therapies, in particular cystic fibrosis transmembrane regulator (CFTR) modulator drugs, have led to significant improvement in the health and well-being of pwCF and may lead to challenges in sampling the lower respiratory tract including to screen for NTM. This review highlights the epidemiology, modes of acquisition, screening and diagnosis, therapeutic approaches in the context of improved clinical status for pwCF, and the clinical application of CFTR modulator therapies.
Collapse
Affiliation(s)
- Andrew Burke
- Department of Thoracic Medicine, The Prince Charles Hospital, Chermside, Queensland, Australia.,Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, Australia
| | - Rachel M Thomson
- Department of Thoracic Medicine, The Prince Charles Hospital, Chermside, Queensland, Australia.,Gallipoli Medical Research Foundation, Greenslopes Private Hospital, Greenslopes, Queensland, Australia
| | - Claire E Wainwright
- Department of Respiratory and Sleep Medicine, Queensland Children's Hospital, South Brisbane, Australia.,Children's Health Research Centre, Faculty of Medicine, The University of Queensland, South Brisbane, Australia
| | - Scott C Bell
- Department of Thoracic Medicine, The Prince Charles Hospital, Chermside, Queensland, Australia.,Children's Health Research Centre, Faculty of Medicine, The University of Queensland, South Brisbane, Australia.,Translational Research Institute, Woolloongabba, Australia
| |
Collapse
|
13
|
Schildkraut JA, Coolen JPM, Severin H, Koenraad E, Aalders N, Melchers WJG, Hoefsloot W, Wertheim HFL, van Ingen J. MGIT Enriched Shotgun Metagenomics for Routine Identification of Nontuberculous Mycobacteria: a Route to Personalized Health Care. J Clin Microbiol 2023; 61:e0131822. [PMID: 36840602 PMCID: PMC10035320 DOI: 10.1128/jcm.01318-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Abstract
Currently, nontuberculous mycobacteria (NTM) are identified using small genomic regions, and species-level identification is often not possible. We introduce a next-generation sequencing (NGS) workflow that identifies mycobacteria to (sub)species level on the basis of the whole genome extracted from enriched shotgun metagenomic data. This technique is used to study the association between genotypes and clinical manifestations to pave the way to more personalized health care. Two sets of clinical isolates (explorative set [n = 212] and validation set [n = 235]) were included. All data were analyzed using a custom pipeline called MyCodentifier. Sequences were matched against a custom hsp65 database (NGS-hsp65) and whole-genome database (NGS-WG) created based on the phylogeny presented by Tortoli et al. (E. Tortoli, T. Fedrizzi, C. J. Meehan, A. Trovato, et al., Infect Genet Evol 56:19-25, 2017, https://doi.org/10.1016/j.meegid.2017.10.013). Lastly, phylogenetic analysis was performed and correlated with clinical manifestation. In the explorative set, we observed 98.6% agreement between the line probe assay and the NGS-hsp65 database. In the validation set, 99.1% agreement between the NGS-WG and NGS-hsp65 databases was seen on the complex level. We identified a cluster of Mycobacterium marinum isolates not represented by the Tortoli et al. phylogeny. Phylogenetic analysis of M. avium complex isolates confirmed misclassification of M. timonense and M. bouchedurhonense and identified subclusters within M. avium although no correlation with clinical manifestation was observed. We performed routine NGS to identify NTM from MGIT enriched shotgun metagenomic data. Phylogenetic analyses identified subtypes of M. avium, but in our set of isolates no correlation with clinical manifestation was found. However, this NGS workflow paves a way for more personalized health care in the future.
Collapse
Affiliation(s)
- Jodie A Schildkraut
- Radboudumc Center for Infectious Diseases, Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Jordy P M Coolen
- Radboudumc Center for Infectious Diseases, Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Heleen Severin
- Radboudumc Center for Infectious Diseases, Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Ellen Koenraad
- Radboudumc Center for Infectious Diseases, Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Nicole Aalders
- Radboudumc Center for Infectious Diseases, Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Willem J G Melchers
- Radboudumc Center for Infectious Diseases, Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Wouter Hoefsloot
- Radboudumc Center for Infectious Diseases, Department of Pulmonary Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Heiman F L Wertheim
- Radboudumc Center for Infectious Diseases, Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Jakko van Ingen
- Radboudumc Center for Infectious Diseases, Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, the Netherlands
| |
Collapse
|
14
|
Mercaldo RA, Marshall JE, Cangelosi GA, Donohue M, Falkinham JO, Fierer N, French JP, Gebert MJ, Honda JR, Lipner EM, Marras TK, Morimoto K, Salfinger M, Stout J, Thomson R, Prevots DR. Environmental risk of nontuberculous mycobacterial infection: Strategies for advancing methodology. Tuberculosis (Edinb) 2023; 139:102305. [PMID: 36706504 PMCID: PMC10023322 DOI: 10.1016/j.tube.2023.102305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 12/27/2022] [Accepted: 01/04/2023] [Indexed: 01/11/2023]
Abstract
The National Institute of Allergy and Infectious Diseases organized a symposium in June 2022, to facilitate discussion of the environmental risks for nontuberculous mycobacteria exposure and disease. The expert researchers presented recent studies and identified numerous research gaps. This report summarizes the discussion and identifies six major areas of future research related to culture-based and culture independent laboratory methods, alternate culture media and culturing conditions, frameworks for standardized laboratory methods, improved environmental sampling strategies, validation of exposure measures, and availability of high-quality spatiotemporal data.
Collapse
Affiliation(s)
- Rachel A Mercaldo
- Division of Intramural Research, Epidemiology and Population Studies Unit, NIAID, NIH, Rockville, MD, USA.
| | - Julia E Marshall
- Division of Intramural Research, Epidemiology and Population Studies Unit, NIAID, NIH, Rockville, MD, USA.
| | - Gerard A Cangelosi
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA.
| | - Maura Donohue
- United States Environmental Protection Agency, Center for Environmental Solutions and Emergency Response, Cincinnati, OH, USA.
| | | | - Noah Fierer
- Department of Ecology and Evolutionary Biology, Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO, USA.
| | - Joshua P French
- Department of Mathematical and Statistical Sciences, University of Colorado Denver, Denver, CO, USA.
| | - Matthew J Gebert
- Department of Ecology and Evolutionary Biology, Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO, USA.
| | - Jennifer R Honda
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA.
| | - Ettie M Lipner
- Division of Intramural Research, Epidemiology and Population Studies Unit, NIAID, NIH, Rockville, MD, USA.
| | - Theodore K Marras
- Department of Medicine, University of Toronto and University Health Network, Toronto, Canada.
| | - Kozo Morimoto
- Division of Clinical Research, Fukujuji Hospital, Japan Anti-Tuberculosis Association, Tokyo, Japan.
| | - Max Salfinger
- College of Public Health & Morsani College of Medicine, University of South Florida, Tampa, FL, USA.
| | - Janet Stout
- Special Pathogens Laboratory, Pittsburgh, PA, USA; Department of Civil and Environmental Engineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Rachel Thomson
- Gallipoli Medical Research Institute & Greenslopes Clinical School, The University of Queensland, Brisbane, Australia.
| | - D Rebecca Prevots
- Division of Intramural Research, Epidemiology and Population Studies Unit, NIAID, NIH, Rockville, MD, USA.
| |
Collapse
|
15
|
Shen Y, Haig SJ, Prussin AJ, LiPuma JJ, Marr LC, Raskin L. Shower water contributes viable nontuberculous mycobacteria to indoor air. PNAS NEXUS 2022; 1:pgac145. [PMID: 36712351 PMCID: PMC9802317 DOI: 10.1093/pnasnexus/pgac145] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 11/07/2022] [Indexed: 11/11/2022]
Abstract
Nontuberculous mycobacteria (NTM) are frequently present in municipal drinking water and building plumbing, and some are believed to cause respiratory tract infections through inhalation of NTM-containing aerosols generated during showering. However, the present understanding of NTM transfer from water to air is insufficient to develop NTM risk mitigation strategies. This study aimed to characterize the contribution of shower water to the abundance of viable NTM in indoor air. Shower water and indoor air samples were collected, and 16S rRNA and rpoB genes were sequenced. The sequencing results showed that running the shower impacted the bacterial community structure and NTM species composition in indoor air by transferring certain bacteria from water to air. A mass balance model combined with NTM quantification results revealed that on average 1/132 and 1/254 of NTM cells in water were transferred to air during 1 hour of showering using a rain and massage showerhead, respectively. A large fraction of the bacteria transferred from water to air were membrane-damaged, i.e. they had compromised membranes based on analysis by live/dead staining and flow cytometry. However, the damaged NTM in air were recoverable as shown by growth in a culture medium mimicking the respiratory secretions of people with cystic fibrosis, implying a potential infection risk by NTM introduced to indoor air during shower running. Among the recovered NTM, Mycobacterium mucogenicum was the dominant species as determined by rpoB gene sequencing. Overall, this study lays the groundwork for future pathogen risk management and public health protection in the built environment.
Collapse
Affiliation(s)
| | | | - Aaron J Prussin
- Department of Civil and Environmental Engineering, Virginia Tech, 418 Durham Hall, Blacksburg, VA 24061, USA
| | - John J LiPuma
- Department of Pediatrics, University of Michigan Medical School, 1500 E. Medical Center Dr., Ann Arbor, MI 48109, USA
| | - Linsey C Marr
- Department of Civil and Environmental Engineering, Virginia Tech, 418 Durham Hall, Blacksburg, VA 24061, USA
| | | |
Collapse
|
16
|
Septic arthritis in a nonprosthetic joint due to Mycobacterium fortuitum: a case report. CURRENT ORTHOPAEDIC PRACTICE 2022. [DOI: 10.1097/bco.0000000000001165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
|
17
|
A Comparison of Three Culture Media for the Detection of Rapid-Growing Nontuberculous Mycobacteria in Environmental Samples. Appl Microbiol 2022. [DOI: 10.3390/applmicrobiol2020026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Nontuberculous mycobacteria (NTM) are common in the environment and certain species can cause serious infections. Improved environmental surveillance methods are needed to combat the increased incidence of NTM disease. Recently, two methods were developed to improve NTM detection. The MYChrOme™ Culture Plate (patent-pending, Phigenics, LLC, Reno, NV, USA) is the first chromogenic medium for rapid-growing NTM detection in water samples. NTM Elite agar (Biomerieux, Marcy-l’Étoile, France), was developed for rapid-growing NTM detection in clinical samples. Fifty water samples (25 potable and 25 non-potable) with three technical replicates were analyzed by each method and Middlebrook 7H11 selective medium (7H11S) (ASTM E2563-07 method modified for water). The MYChrOme method was overall equivalent to or better than 7H11S medium and NTM Elite agar for the detection of rapid-growing NTM in potable water. All three methods detected similar amounts of NTM in non-potable water samples. The chromogenic property of MYChrOme allowed NTM colonies to be quickly identified and differentiated from other bacteria. Additional analysis is required for colony confirmation on 7H11S medium and NTM Elite agar. The use of innovative environmental NTM diagnostics, in addition to proper water management, can greatly reduce the risk of NTM disease.
Collapse
|
18
|
Morgado S, Ramos NDV, Pereira BBDN, Freitas F, Fonseca ÉLD, Vicente AC. Multidrug-resistant Mycolicibacterium fortuitum infection in a companion cat (Felis silvestris catus) in Brazil. Access Microbiol 2022; 4:000317. [PMID: 35355875 PMCID: PMC8941956 DOI: 10.1099/acmi.0.000317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 12/09/2021] [Indexed: 11/24/2022] Open
Abstract
Mycolicibacterium fortuitum is a fast-growing bacterium and an opportunistic pathogen implicated in human and animal infections. Here we report the first case and genetic characterization of a strain of M. fortuitum isolated from skin lesions of a companion cat with atypical cutaneous mycobacteriosis in Brazil. In addition, the genome of this strain was sequenced, representing the first genome of this opportunistic pathogen isolated from an animal infection. The in silico and in vitro analysis regarding antibiotic resistance of this strain showed an intrinsic multiresistance antibiotic profile. However, this strain showed sensitivity to amikacin and ciprofloxacin, and the cat was treated long-term with these drugs.
Collapse
Affiliation(s)
- Sergio Morgado
- Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Laboratório de Genética Molecular de Microrganismos, Rio de Janeiro, Brazil
| | - Nilcéia de Veiga Ramos
- Universidade de Vassouras, Faculdade de Ciências Médicas de Maricá, Rio de Janeiro, Brazil
| | | | - Fernanda Freitas
- Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Laboratório de Genética Molecular de Microrganismos, Rio de Janeiro, Brazil
| | - Érica Lourenço da Fonseca
- Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Laboratório de Genética Molecular de Microrganismos, Rio de Janeiro, Brazil
| | - Ana Carolina Vicente
- Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Laboratório de Genética Molecular de Microrganismos, Rio de Janeiro, Brazil
| |
Collapse
|
19
|
Morgado S, Ramos NDV, Freitas F, da Fonseca ÉL, Vicente AC. Mycolicibacterium fortuitum genomic epidemiology, resistome and virulome. Mem Inst Oswaldo Cruz 2022; 116:e210247. [PMID: 35019071 PMCID: PMC8752049 DOI: 10.1590/0074-02760210247] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 10/13/2021] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Mycolicibacterium fortuitum is an opportunistic pathogen associated with human and animal infection worldwide. Studies concerning this species are mainly represented by case reports, some of them addressing drug susceptibility with a focus on a specific geographic region, so there is a gap in relation to the global epidemiological scenario. OBJECTIVES We aimed determine the global epidemiological scenario of M. fortuitum and analyse its traits associated with pathogenicity. METHODS Based on publicly available genomes of M. fortuitum and a genome from Brazil (this study), we performed a genomic epidemiology analysis and in silico and in vitro characterisation of the resistome and virulome of this species. FINDINGS Three main clusters were defined, one including isolates from the environment, human and animal infections recovered over nearly a century. An apparent intrinsic resistome comprises mechanisms associated with macrolides, beta-lactams, aminoglycosides and antitubercular drugs such as rifampin. Besides, the virulome presented Type VII secretion systems (T7SS), including ESX-1, ESX-3, ESX-4 and ESX-4-bis, some of which play a role on the virulence of Mycobacteriaceae species. MAIN CONCLUSIONS Here, M. fortuitum was revealed as a reservoir of an expressive intrinsic resistome, as well as a virulome that may contribute to its success as a global opportunist pathogen.
Collapse
Affiliation(s)
- Sergio Morgado
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Genética Molecular de Microrganismos, Rio de Janeiro, RJ, Brasil
| | | | - Fernanda Freitas
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Genética Molecular de Microrganismos, Rio de Janeiro, RJ, Brasil
| | - Érica Lourenço da Fonseca
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Genética Molecular de Microrganismos, Rio de Janeiro, RJ, Brasil
| | - Ana Carolina Vicente
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Genética Molecular de Microrganismos, Rio de Janeiro, RJ, Brasil
| |
Collapse
|
20
|
Foote SL, Lipner EM, Prevots DR, Ricotta EE. Environmental predictors of pulmonary nontuberculous mycobacteria (NTM) sputum positivity among persons with cystic fibrosis in the state of Florida. PLoS One 2021; 16:e0259964. [PMID: 34882686 PMCID: PMC8659685 DOI: 10.1371/journal.pone.0259964] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 11/01/2021] [Indexed: 11/19/2022] Open
Abstract
Nontuberculous mycobacteria (NTM) are opportunistic human pathogens that are commonly found in soil and water, and exposure to these organisms may cause pulmonary nontuberculous mycobacterial disease. Persons with cystic fibrosis (CF) are at high risk for developing pulmonary NTM infections, and studies have shown that prolonged exposure to certain environments can increase the risk of pulmonary NTM. It is therefore important to determine the risk associated with different geographic areas. Using annualized registry data obtained from the Cystic Fibrosis Foundation Patient Registry for 2010 through 2017, we conducted a geospatial analysis of NTM infections among persons with CF in Florida. A Bernoulli model in SaTScan was used to identify clustering of ZIP codes with higher than expected numbers of NTM culture positive individuals. Generalized linear mixed models with a binomial distribution were used to test the association of environmental variables and NTM culture positivity. We identified a significant cluster of M. abscessus and predictors of NTM sputum positivity, including annual precipitation and soil mineral levels.
Collapse
Affiliation(s)
- Sydney L. Foote
- Office of Data Science and Emerging Technologies, Office of Science Management and Operations, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Rockville, MD, United States of America
| | - Ettie M. Lipner
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, United States of America
- Department of Epidemiology, Colorado School of Public Health, Aurora, CO, United States of America
| | - D. Rebecca Prevots
- Division of Intramural Research, Epidemiology and Population Studies Unit, NIAID, NIH, Rockville, MD, United States of America
| | - Emily E. Ricotta
- Division of Intramural Research, Epidemiology and Population Studies Unit, NIAID, NIH, Rockville, MD, United States of America
- * E-mail:
| |
Collapse
|
21
|
Ahn K, Kim YK, Hwang GY, Cho H, Uh Y. Continued Upward Trend in Non-Tuberculous Mycobacteria Isolation over 13 Years in a Tertiary Care Hospital in Korea. Yonsei Med J 2021; 62:903-910. [PMID: 34558869 PMCID: PMC8470563 DOI: 10.3349/ymj.2021.62.10.903] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 07/23/2021] [Accepted: 07/23/2021] [Indexed: 12/02/2022] Open
Abstract
PURPOSE Despite decreased prevalence of tuberculosis, the incidence of the diseases associated with nontuberculous mycobacteria (NTM) has been increasing in South Korea and around the world. The present retrospective study was conducted to determine longitudinal changes in the epidemiology and distribution of NTM over 13 years at a tertiary care hospital in Korea. MATERIALS AND METHODS We retrospectively analyzed data on Mycobacterium species over 13 years (January 2007 to December 2019) by utilizing the laboratory information system. Mycobacterium species were identified using biochemical tests and PCR-restriction fragment length polymorphism and Mycobacteria GenoBlot assays. RESULTS After excluding duplicates from the initial pool of 17996 mycobacterial isolates, 7674 strains were analyzed and 2984 (38.9%) NTM were isolated. The proportion of NTM continuously increased over the 13-year period, from 17.0% in 2007 to 57.5% in 2019. Among the NTM isolates, the most common species were Mycobacterium intracellulare (50.6%), M. avium (18.3%), M. fortuitumcomplex (4.9%), M. abscessus (4.5%), M. gordonae (3.3%), M. kansasii (1.1%), M. chelonae (1.0%), and M. massiliense (0.9%). In patients over the age of 70 years, the proportion of NTM among the isolates increased from 26.6% in 2007 to 62.0% in 2019, and that of M. intracellulare isolates among the NTM increased from 13.9% (11/79) in 2007 to 37.4% (175/468) in 2019. CONCLUSION The number of NTM isolates continuously increased over the study period, and the increase in the proportion of M.intracellulare in patients aged over 70 years was notable.
Collapse
Affiliation(s)
- Kwangjin Ahn
- Department of Public Health Inspection, Armed Forces Medical Research Institute, Daejeon, Korea
| | - Young Keun Kim
- Department of Internal Medicine, Yonsei University Wonju College of Medicine, Wonju, Korea
| | - Gyu Yel Hwang
- Department of Laboratory Medicine, Yonsei University Wonju College of Medicine, Wonju, Korea
| | - Hyunmi Cho
- Department of Laboratory Medicine, Yonsei University Wonju College of Medicine, Wonju, Korea
| | - Young Uh
- Department of Laboratory Medicine, Yonsei University Wonju College of Medicine, Wonju, Korea.
| |
Collapse
|
22
|
Mugetti D, Varello K, Pastorino P, Tomasoni M, Menconi V, Bozzetta E, Dondo A, Prearo M. Investigation of Potential Reservoirs of Non-Tuberculous Mycobacteria in a European Sea Bass ( Dicentrarchus labrax) Farm. Pathogens 2021; 10:pathogens10081014. [PMID: 34451479 PMCID: PMC8401025 DOI: 10.3390/pathogens10081014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 08/02/2021] [Accepted: 08/06/2021] [Indexed: 11/16/2022] Open
Abstract
Fish mycobacteriosis is a widespread global problem caused by species of non-tuberculous mycobacteria (NTM). Mycobacterium marinum is one of the species most often involved in disease episodes of aquarium and farmed fish. Since there is currently no available effective therapy or vaccine, a prompt search for routes of entry is key to limiting the damage induced by the disease. Here we report a case of mycobacteriosis follow up in a European sea bass (Dicentrarchus labrax) farm located in Northern Italy, in which environmental samples and newly added fish batches were analyzed. Samples from fish present on the farm, sediment, and periphyton all resulted positive for M. marinum, whereas the new fish batches and the water samples resulted negative. The environmental resistance of NTM (alcohol-acid resistance, biofilm formation) and the lack of prophylactic and therapeutic strategies make these diseases difficult to manage. Prompt identification of biotic and abiotic reservoirs, combined with good zootechnical hygiene practices, are the most effective measures to control fish mycobacteriosis in intensive farms.
Collapse
|
23
|
Victoria L, Gupta A, Gómez JL, Robledo J. Mycobacterium abscessus complex: A Review of Recent Developments in an Emerging Pathogen. Front Cell Infect Microbiol 2021; 11:659997. [PMID: 33981630 PMCID: PMC8108695 DOI: 10.3389/fcimb.2021.659997] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 04/07/2021] [Indexed: 01/04/2023] Open
Abstract
Mycobacterium abscessus complex (MABC) is one of the most clinically relevant species among nontuberculous mycobacteria. MABC's prevalence has increased over the last two decades. Although these changes can be explained by improvements in microbiological and molecular techniques for identifying species and subspecies, a higher prevalence of chronic lung diseases may contribute to higher rates of MABC. High rates of antimicrobial resistance are seen in MABC, and patients experience multiple relapses with low cure rates. This review aims to integrate existing knowledge about MABC epidemiology, microbiological identification and familiarize readers with molecular mechanisms of resistance and therapeutic options for pulmonary infections with MABC.
Collapse
Affiliation(s)
- Laura Victoria
- Laboratory of Bacteriology and Mycobacteria, Corporación para Investigaciones Biológicas (CIB), Medellín, Colombia.,Escuela de Ciencias de la Salud, Universidad Pontificia Bolivariana, Medellín, Colombia
| | - Amolika Gupta
- Pulmonary, Critical Care and Sleep Medicine Section, Yale University School of Medicine, New Haven, CT, United States
| | - Jose Luis Gómez
- Pulmonary, Critical Care and Sleep Medicine Section, Yale University School of Medicine, New Haven, CT, United States
| | - Jaime Robledo
- Laboratory of Bacteriology and Mycobacteria, Corporación para Investigaciones Biológicas (CIB), Medellín, Colombia.,Escuela de Ciencias de la Salud, Universidad Pontificia Bolivariana, Medellín, Colombia
| |
Collapse
|
24
|
Gene Sequencing and Phylogenetic Analysis: Powerful Tools for an Improved Diagnosis of Fish Mycobacteriosis Caused by Mycobacterium fortuitum Group Members. Microorganisms 2021; 9:microorganisms9040797. [PMID: 33920196 PMCID: PMC8068823 DOI: 10.3390/microorganisms9040797] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/13/2021] [Accepted: 04/08/2021] [Indexed: 11/30/2022] Open
Abstract
The Mycobacterium fortuitum group (MFG) consists of about 15 species of fast-growing nontuberculous mycobacteria (NTM). These globally distributed microorganisms can cause diseases in humans and animals, especially fish. The increase in the number of species belonging to MFG and the diagnostic techniques panel do not allow to clarify their real clinical significance. In this study, biomolecular techniques were adopted for species determination of 130 isolates derived from fish initially identified through biochemical tests as NTM belonging to MFG. Specifically, gene sequencing and phylogenetic analysis were used based on a fragment of the gene encoding the 65 KDa heat shock protein (hsp65). The analyzes made it possible to confirm that all the isolates belong to MFG, allowing to identify the strains at species level. Phylogenetic analysis substantially confirmed what was obtained by gene sequencing, except for six strains; this is probably due to the sequences present in NCBI database. Although the methodology used cannot represent a univocal identification system, this study has allowed us to evaluate its effectiveness as regards the species of MFG. Future studies will be necessary to apply these methods with other gene fragments and to clarify the real pathogenic significance of the individual species of this group of microorganisms.
Collapse
|
25
|
Biofilm Degradation of Nontuberculous Mycobacteria Formed on Stainless Steel Following Treatment with Immortelle (Helichrysum italicum) and Common Juniper (Juniperus communis) Essential Oils. Processes (Basel) 2021. [DOI: 10.3390/pr9020362] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Nontuberculous mycobacteria, like other opportunistic premise plumbing pathogens, produce resistant biofilms on various surfaces in the plumbing system including pipes, tanks, and fittings. Since standard methods of water disinfection are ineffective in eradicating biofilms, research into new agents is necessary. Essential oils (EOs) have great potential as anti-biofilm agents. Therefore, the purpose of this research was to investigate the potential anti-biofilm effect of common juniper (Juniperus communis) and immortelle (Helichrysum italicum) EOs. Minimum inhibitory concentrations (MIC), minimum bactericidal concentrations (MBC), and minimum effective concentrations of EOs on Mycobacterium avium, M. intracellulare, and M. gordonae were tested. Additionally, biofilms on the surface of a stainless steel disc were treated with single or mixed concentration of EOs, in order to investigate their degeneration via the bacterial count and confocal laser scanning microscopy (CLSM). H. italicum EO showed the strongest biofilm degradation ability against all Mycobacteria strains that were tested. The strongest effect in the biofilm degradation after the single or mixed applications of EOs was observed against M. gordonae, followed by M. avium. The most resistant was the M. intracellulare biofilm. Synergistic combinations of J. communis and H. italicum EOs therefore seem to be an effective substance in biofilm degradation for use in small water systems such as baths or hot tubs.
Collapse
|
26
|
Thomson RM, Furuya-Kanamori L, Coffey C, Bell SC, Knibbs LD, Lau CL. Influence of climate variables on the rising incidence of nontuberculous mycobacterial (NTM) infections in Queensland, Australia 2001-2016. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 740:139796. [PMID: 32563864 DOI: 10.1016/j.scitotenv.2020.139796] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 04/22/2020] [Accepted: 05/27/2020] [Indexed: 06/11/2023]
Abstract
UNLABELLED International reports indicate a rising incidence of nontuberculous mycobacterial (NTM) disease. Many infectious diseases have seasonal variation in incidence, and major weather events and climate change have been implicated. The aim of this study was to explore the relationship between climate variables and NTM incident cases in Queensland, Australia. METHODS NTM data were obtained from the Queensland notifiable conditions database for the period 2001-2016. Rainfall and temperature data were obtained from the Australian Bureau of Meteorology. Poisson regression models were used to assess notification rates (incidence cases per 100,000 population) over time and to estimate incidence rate ratios (IRR). Cross correlation coefficients were used to examine the relationship between rainfall and temperature data and NTM incidence over time in each Hospital and Health Service (HHS). RESULTS 12,219 NTM cases were reported. The most common species was M. intracellulare (39.1%), followed by M. avium (9.8%), M abscessus (8.5%), M. fortuitum (8.3%), M. chelonae (3.3%), and M. kansasii (2.4%). The estimated incidence rate increased from 11.10 (95% CI 8.10-15.22) in 2001 to 25.88 (95%CI 21.78-30.73) per 100,000 in 2016. The estimated IRR increased for all common species, except M. kansasii. Although increased IRRs were observed for most NTM species, geospatial heterogeneity was observed. The effect of rainfall and temperature on NTM incidence differed between species and geographic regions. CONCLUSIONS The incidence of NTM infections increased between 2001 and 2016. Variations in temperature and rainfall may play a role in environmental exposure to some species of NTM. Spatial variation in IRR suggests that there may also be other environmental factors that influence transmission.
Collapse
Affiliation(s)
- Rachel M Thomson
- Gallipoli Medical Research Institute, University of Queensland, Brisbane, Australia.
| | - Luis Furuya-Kanamori
- Research School of Population Health, Australian National University, Canberra, Australia
| | - Cushla Coffey
- Research School of Population Health, Australian National University, Canberra, Australia
| | - Scott C Bell
- The Prince Charles Hospital, Faculty of Medicine, University of Queensland and Translational Research Institute, Brisbane, Australia
| | - Luke D Knibbs
- School of Public Health, University of Queensland, Brisbane, Australia
| | - Colleen L Lau
- Research School of Population Health, Australian National University, Canberra, Australia
| |
Collapse
|
27
|
Pereira AC, Ramos B, Reis AC, Cunha MV. Non-Tuberculous Mycobacteria: Molecular and Physiological Bases of Virulence and Adaptation to Ecological Niches. Microorganisms 2020; 8:microorganisms8091380. [PMID: 32916931 PMCID: PMC7563442 DOI: 10.3390/microorganisms8091380] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 09/06/2020] [Accepted: 09/07/2020] [Indexed: 12/15/2022] Open
Abstract
Non-tuberculous mycobacteria (NTM) are paradigmatic colonizers of the total environment, circulating at the interfaces of the atmosphere, lithosphere, hydrosphere, biosphere, and anthroposphere. Their striking adaptive ecology on the interconnection of multiple spheres results from the combination of several biological features related to their exclusive hydrophobic and lipid-rich impermeable cell wall, transcriptional regulation signatures, biofilm phenotype, and symbiosis with protozoa. This unique blend of traits is reviewed in this work, with highlights to the prodigious plasticity and persistence hallmarks of NTM in a wide diversity of environments, from extreme natural milieus to microniches in the human body. Knowledge on the taxonomy, evolution, and functional diversity of NTM is updated, as well as the molecular and physiological bases for environmental adaptation, tolerance to xenobiotics, and infection biology in the human and non-human host. The complex interplay between individual, species-specific and ecological niche traits contributing to NTM resilience across ecosystems are also explored. This work hinges current understandings of NTM, approaching their biology and heterogeneity from several angles and reinforcing the complexity of these microorganisms often associated with a multiplicity of diseases, including pulmonary, soft-tissue, or milliary. In addition to emphasizing the cornerstones of knowledge involving these bacteria, we identify research gaps that need to be addressed, stressing out the need for decision-makers to recognize NTM infection as a public health issue that has to be tackled, especially when considering an increasingly susceptible elderly and immunocompromised population in developed countries, as well as in low- or middle-income countries, where NTM infections are still highly misdiagnosed and neglected.
Collapse
Affiliation(s)
- André C. Pereira
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal; (A.C.P.); (B.R.); (A.C.R.)
- Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Beatriz Ramos
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal; (A.C.P.); (B.R.); (A.C.R.)
- Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Ana C. Reis
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal; (A.C.P.); (B.R.); (A.C.R.)
- Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Mónica V. Cunha
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal; (A.C.P.); (B.R.); (A.C.R.)
- Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal
- Correspondence: ; Tel.: +351-217-500-000 (ext. 22461)
| |
Collapse
|
28
|
Moon P, Guillaumin E, Chan ED. Non-tuberculous mycobacterial lung disease due to multiple "minor" risk factors: an illustrative case and a review of these "lesser elements". J Thorac Dis 2020; 12:4960-4972. [PMID: 33145070 PMCID: PMC7578471 DOI: 10.21037/jtd-20-986] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
| | | | - Edward D Chan
- Department of Academic Affairs, National Jewish Health, Denver, CO, USA.,Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.,Rocky Mountain Regional Veterans Affairs Medical Center, Aurora, CO, USA
| |
Collapse
|
29
|
The Epidemiology of Extrapulmonary Non-tuberculous Mycobacterial Infection in a Pediatric Population. Pediatr Infect Dis J 2020; 39:671-677. [PMID: 32235244 DOI: 10.1097/inf.0000000000002658] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND Nontuberculous mycobacteria (NTM) are ubiquitous in the environment and a well-known cause of lymphadenitis, skin and soft tissue infections. The aim of this study was to evaluate the epidemiology of extrapulmonary pediatric NTM infections occurring from 2000 to 2017 in Queensland, Australia. METHODS All cases of NTM and TB are notifiable under the Queensland Public Health Act (2005) and associated regulations (2005). Data from 2000 to 2017 inclusive was collected from the Notifiable Conditions Database, a laboratory based notification system that covers private and public laboratory systems. Pediatric population demographic data were obtained from the Australian Bureau of Statistics by researching the number of children 0-14 years of age in Queensland from 2000 to 2017; both annual and averaged population was determined. The statistical software SPSS and Tableau was used for analysis. RESULTS The mean age of diagnosis was 2.5 years with a majority of the cohort being women. Mycobacterium avium was the most commonly diagnosed pathogen. Geographic regions with the highest numbers of cases were predominantly tropical and coastal areas. M. haemophilum emerged as a more common pathogen from 2011 following a period of major flooding. CONCLUSION Characteristics of the cohort of children susceptible to NTM disease appears consistent with previous reports. However, changes in the epidemiology of NTM infection (such as incidence, species, and geographic distribution) in children may be linked to environmental and weather factors.
Collapse
|
30
|
Zhou L, Xu D, Liu H, Wan K, Wang R, Yang Z. Trends in the Prevalence and Antibiotic Resistance of Non-tuberculous Mycobacteria in Mainland China, 2000-2019: Systematic Review and Meta-Analysis. Front Public Health 2020; 8:295. [PMID: 32850570 PMCID: PMC7399041 DOI: 10.3389/fpubh.2020.00295] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Accepted: 06/04/2020] [Indexed: 12/16/2022] Open
Abstract
Background: China is a high-burden country of tuberculosis. The proportion of diseases caused by non-tuberculous mycobacteria (NTM) has increased, seriously affecting the prevention, control, and management of tuberculosis (TB) and posing a significant threat to human health. However, there is a lack of an organized monitoring system for NTM such as that used for tuberculosis. Comprehensive data on patient susceptibility, dominant species, and drug resistance profiles are needed to improve the treatment protocols and the management of NTM. Methods: Primary research reports of NTM clinical specimens from mainland China published between January 1, 2000 and May 31, 2019 were retrieved from four online resources (BIOSIS, Embase, PubMed, and Web of Science) and three Chinese medical literature databases (CNKI, Wanfang, and Vip) as the Preferred Reporting Items for Systematic Reviews and Meta-Analyses. Results: In total, 339 publications were included in the systematic review, 129 were used in the drug susceptibility analysis, and 95 were used in the meta-analysis. Traditional culture using Lowenstein-Jensen slants combined with P-nitrobenzene acid and thiophene-2-carboxylic acid hydrazine differential medium and proportional method was most commonly used for the isolation, identification, and drug susceptibility testing of NTM in China. The crude isolation rate for NTM among TB suspected cases was 4.66-5.78%, while the proportion of NTM among Mycobacterium isolates was 11.57%. Mycobacterium abscessus and Mycobacterium avium complex were the most common clinical NTM species. NTM only showed general sensitivity to ethambutol, linezolid, clofazimine, amikacin, tobramycin, and clarithromycin. Conclusions: The prevalence of NTM in China has shown a decreasing trend. M. abscessus was replaced as the dominant species by Mycobacterium intracellulare over the course of the study. The geographic diversity of different species showed the effects of environmental and economic factors on the distribution of NTM and indicated that there were important factors still not identified. While there were only a limited number of antibiotics to which NTM showed any sensitivity, the drug resistance profiles of the isolates were highly variable and thus more caution should be taken when empirically treating NTM infection.
Collapse
Affiliation(s)
- Lei Zhou
- College of Pharmacy, Guizhou University, Guiyang, China.,State Key Laboratory for Infectious Disease Prevention and Control, Chinese Centre for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Da Xu
- State Key Laboratory for Infectious Disease Prevention and Control, Chinese Centre for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China.,Guangdong Key Laboratory for Diagnosis and Treatment of Emerging Infectious Diseases, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, China
| | - Hancan Liu
- State Key Laboratory for Infectious Disease Prevention and Control, Chinese Centre for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China.,Guangdong Key Laboratory for Diagnosis and Treatment of Emerging Infectious Diseases, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, China
| | - Kanglin Wan
- State Key Laboratory for Infectious Disease Prevention and Control, Chinese Centre for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China.,Guangdong Key Laboratory for Diagnosis and Treatment of Emerging Infectious Diseases, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, China
| | - Ruibai Wang
- State Key Laboratory for Infectious Disease Prevention and Control, Chinese Centre for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China.,Guangdong Key Laboratory for Diagnosis and Treatment of Emerging Infectious Diseases, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, China
| | - Zaichang Yang
- College of Pharmacy, Guizhou University, Guiyang, China
| |
Collapse
|
31
|
Busatto C, Vianna JS, Silva ABS, Basso R, Silveira J, Groll AV, Ramis IB, Silva PEAD. Nontuberculous mycobacteria in patients with suspected tuberculosis and the genetic diversity of Mycobacterium avium in the extreme south of Brazil. ACTA ACUST UNITED AC 2020; 46:e20190184. [PMID: 32402014 PMCID: PMC7462694 DOI: 10.36416/1806-3756/e20190184] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 08/04/2019] [Indexed: 11/26/2022]
Abstract
Objective: Nontuberculous mycobacteria (NTM) are a heterogeneous group of bacteria that are widely distributed in nature and associated with opportunistic infections in humans. The aims of this study were to identify NTM in patients with suspected tuberculosis who presented positive cultures and to evaluate the genetic diversity of strains identified as Mycobacterium avium. Methods: We studied pulmonary and extrapulmonary samples obtained from 1,248 patients. The samples that tested positive on culture and negative for the M. tuberculosis complex by molecular identification techniques were evaluated by detection of the hsp65 and rpoB genes and sequencing of conserved fragments of these genes. All strains identified as M. avium were genotyped using the eight-locus mycobacterial interspersed repetitive unit-variable-number tandem-repeat method. Results: We found that NTM accounted for 25 (7.5%) of the 332 mycobacteria isolated. Of those 25, 18 (72%) were M. avium, 5 (20%) were M. abscessus, 1 (4%) was M. gastri, and 1 (4%) was M. kansasii. The 18 M. avium strains showed high diversity, only two strains being genetically related. Conclusions: These results highlight the need to consider the investigation of NTM in patients with suspected active tuberculosis who present with positive cultures, as well as to evaluate the genetic diversity of M. avium strains.
Collapse
Affiliation(s)
- Caroline Busatto
- Núcleo de Pesquisa em Microbiologia Médica, Faculdade de Medicina, Universidade Federal do Rio Grande, Rio Grande, RS, Brazil
| | - Júlia Silveira Vianna
- Núcleo de Pesquisa em Microbiologia Médica, Faculdade de Medicina, Universidade Federal do Rio Grande, Rio Grande, RS, Brazil
| | - Ana Barbara Scholante Silva
- Núcleo de Pesquisa em Microbiologia Médica, Faculdade de Medicina, Universidade Federal do Rio Grande, Rio Grande, RS, Brazil
| | - Rossana Basso
- Faculdade de Medicina, Universidade Federal do Rio Grande, Rio Grande, RS, Brazil
| | - Jussara Silveira
- Faculdade de Medicina, Universidade Federal do Rio Grande, Rio Grande, RS, Brazil
| | - Andrea Von Groll
- Núcleo de Pesquisa em Microbiologia Médica, Faculdade de Medicina, Universidade Federal do Rio Grande, Rio Grande, RS, Brazil
| | - Ivy Bastos Ramis
- Núcleo de Pesquisa em Microbiologia Médica, Faculdade de Medicina, Universidade Federal do Rio Grande, Rio Grande, RS, Brazil
| | - Pedro Eduardo Almeida da Silva
- Núcleo de Pesquisa em Microbiologia Médica, Faculdade de Medicina, Universidade Federal do Rio Grande, Rio Grande, RS, Brazil
| |
Collapse
|
32
|
Chin KL, Sarmiento ME, Alvarez-Cabrera N, Norazmi MN, Acosta A. Pulmonary non-tuberculous mycobacterial infections: current state and future management. Eur J Clin Microbiol Infect Dis 2020; 39:799-826. [PMID: 31853742 PMCID: PMC7222044 DOI: 10.1007/s10096-019-03771-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Accepted: 11/18/2019] [Indexed: 12/11/2022]
Abstract
Currently, there is a trend of increasing incidence in pulmonary non-tuberculous mycobacterial infections (PNTM) together with a decrease in tuberculosis (TB) incidence, particularly in developed countries. The prevalence of PNTM in underdeveloped and developing countries remains unclear as there is still a lack of detection methods that could clearly diagnose PNTM applicable in these low-resource settings. Since non-tuberculous mycobacteria (NTM) are environmental pathogens, the vicinity favouring host-pathogen interactions is known as important predisposing factor for PNTM. The ongoing changes in world population, as well as socio-political and economic factors, are linked to the rise in the incidence of PNTM. Development is an important factor for the improvement of population well-being, but it has also been linked, in general, to detrimental environmental consequences, including the rise of emergent (usually neglected) infectious diseases, such as PNTM. The rise of neglected PNTM infections requires the expansion of the current efforts on the development of diagnostics, therapies and vaccines for mycobacterial diseases, which at present, are mainly focused on TB. This review discuss the current situation of PNTM and its predisposing factors, as well as the efforts and challenges for their control.
Collapse
Affiliation(s)
- Kai Ling Chin
- Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah (UMS), Kota Kinabalu, Sabah, Malaysia.
| | - Maria E Sarmiento
- School of Health Sciences, Universiti Sains Malaysia (USM), Kubang Kerian, Kelantan, Malaysia
| | - Nadine Alvarez-Cabrera
- Center for Discovery and Innovation (CDI), Hackensack Meridian School of Medicine at Seton Hall University, Nutley, NJ, USA
| | - Mohd Nor Norazmi
- School of Health Sciences, Universiti Sains Malaysia (USM), Kubang Kerian, Kelantan, Malaysia
| | - Armando Acosta
- School of Health Sciences, Universiti Sains Malaysia (USM), Kubang Kerian, Kelantan, Malaysia.
| |
Collapse
|
33
|
Tremblay EE, Stewart BD, Beal SG. Educational Case: Identification of Pulmonary Mycobacteria. Acad Pathol 2020; 7:2374289520901827. [PMID: 32110720 PMCID: PMC7001141 DOI: 10.1177/2374289520901827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 10/21/2019] [Accepted: 01/01/2020] [Indexed: 11/29/2022] Open
Abstract
The following fictional case is intended as a learning tool within the Pathology Competencies for Medical Education (PCME), a set of national standards for teaching pathology. These are divided into three basic competencies: Disease Mechanisms and Processes, Organ System Pathology, and Diagnostic Medicine and Therapeutic Pathology. For additional information, and a full list of learning objectives for all three competencies, seehttp://journals.sagepub.com/doi/10.1177/2374289517715040.1
Collapse
Affiliation(s)
| | - Brian D Stewart
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL, USA
| | - Stacy G Beal
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL, USA
| |
Collapse
|
34
|
Nontuberculous Mycobacterium. Respir Med 2020. [DOI: 10.1007/978-3-030-42382-7_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
35
|
Kloth H, Elbadawi LI, Bateman A, Louison L, Shrivastwa N. Notes from the Field: Hospital Water Contamination Associated with a Pseudo-Outbreak of Mycobacterium porcinum — Wisconsin, 2016–2018. MMWR. MORBIDITY AND MORTALITY WEEKLY REPORT 2019; 68:1149. [PMID: 31830010 PMCID: PMC6919292 DOI: 10.15585/mmwr.mm6849a4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
|
36
|
Ibekwe AM, Murinda SE. Linking Microbial Community Composition in Treated Wastewater with Water Quality in Distribution Systems and Subsequent Health Effects. Microorganisms 2019; 7:microorganisms7120660. [PMID: 31817873 PMCID: PMC6955928 DOI: 10.3390/microorganisms7120660] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 12/04/2019] [Accepted: 12/05/2019] [Indexed: 12/12/2022] Open
Abstract
The increases in per capita water consumption, coupled in part with global climate change have resulted in increased demands on available freshwater resources. Therefore, the availability of safe, pathogen-free drinking water is vital to public health. This need has resulted in global initiatives to develop sustainable urban water infrastructure for the treatment of wastewater for different purposes such as reuse water for irrigation, and advanced waste water purification systems for domestic water supply. In developed countries, most of the water goes through primary, secondary, and tertiary treatments combined with disinfectant, microfiltration (MF), reverse osmosis (RO), etc. to produce potable water. During this process the total bacterial load of the water at different stages of the treatment will decrease significantly from the source water. Microbial diversity and load may decrease by several orders of magnitude after microfiltration and reverse osmosis treatment and falling to almost non-detectable levels in some of the most managed wastewater treatment facilities. However, one thing in common with the different end users is that the water goes through massive distribution systems, and the pipes in the distribution lines may be contaminated with diverse microbes that inhabit these systems. In the main distribution lines, microbes survive within biofilms which may contain opportunistic pathogens. This review highlights the role of microbial community composition in the final effluent treated wastewater, biofilms formation in the distribution systems as the treated water goes through, and the subsequent health effects from potential pathogens associated with poorly treated water. We conclude by pointing out some basic steps that may be taken to reduce the accumulation of biofilms in the water distribution systems.
Collapse
Affiliation(s)
- Abasiofiok Mark Ibekwe
- US Salinity Laboratory, USDA-ARS, 450 W. Big Springs Rd., Riverside, CA 92507, USA
- Correspondence: ; Tel.: +951-369-4828
| | - Shelton E. Murinda
- Animal and Veterinary Sciences Department, Center for Antimicrobial Research and Food Safety, California State Polytechnic University, Pomona, CA 91768, USA;
| |
Collapse
|
37
|
Matsumoto Y, Kinjo T, Motooka D, Nabeya D, Jung N, Uechi K, Horii T, Iida T, Fujita J, Nakamura S. Comprehensive subspecies identification of 175 nontuberculous mycobacteria species based on 7547 genomic profiles. Emerg Microbes Infect 2019; 8:1043-1053. [PMID: 31287781 PMCID: PMC6691804 DOI: 10.1080/22221751.2019.1637702] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The prevalence of nontuberculous mycobacteria (NTM) pulmonary diseases has been increasing worldwide. NTM consist of approximately 200 species and distinguishing between them at the subspecies level is critical to treatment. In this study, we sequenced 63 NTM genomes, 27 of which were newly determined, by hybrid assembly using sequencers from Illumina and Oxford Nanopore Technologies (ONT). This analysis expanded the available genomic data to 175 NTM species and redefined their subgenus classification. We also developed a novel multi-locus sequence typing (MLST) database based on 184 genes from 7547 assemblies and an identification software, mlstverse, which can also be used for detecting other bacteria given a suitable MLST database. This method showed the highest sensitivity and specificity amongst conventional methods and demonstrated the capacity for rapid detection of NTM, 10 min of sequencing of the ONT MinION being sufficient. Application of this methodology could improve disease epidemiology and increase the cure rates of NTM diseases.
Collapse
Affiliation(s)
- Yuki Matsumoto
- a Department of Infection Metagenomics, Genome Information Research Center, Research Institute for Microbial Diseases , Osaka University , Suita , Japan
| | - Takeshi Kinjo
- b Department of Infectious, Respiratory, and Digestive Medicine, Graduate School of Medicine , University of the Ryukyus , Nakagami-gun , Japan
| | - Daisuke Motooka
- a Department of Infection Metagenomics, Genome Information Research Center, Research Institute for Microbial Diseases , Osaka University , Suita , Japan.,c Laboratory of Pathogen Detection and Identification, International Research Center for Infectious Diseases, Research Institute for Microbial Diseases , Osaka University , Suita , Japan
| | - Daijiro Nabeya
- b Department of Infectious, Respiratory, and Digestive Medicine, Graduate School of Medicine , University of the Ryukyus , Nakagami-gun , Japan
| | - Nicolas Jung
- a Department of Infection Metagenomics, Genome Information Research Center, Research Institute for Microbial Diseases , Osaka University , Suita , Japan
| | - Kohei Uechi
- b Department of Infectious, Respiratory, and Digestive Medicine, Graduate School of Medicine , University of the Ryukyus , Nakagami-gun , Japan.,d Division of Clinical Laboratory and Blood Transfusion , University of the Ryukyus Hospital , Nakagami-gun , Japan
| | - Toshihiro Horii
- a Department of Infection Metagenomics, Genome Information Research Center, Research Institute for Microbial Diseases , Osaka University , Suita , Japan
| | - Tetsuya Iida
- a Department of Infection Metagenomics, Genome Information Research Center, Research Institute for Microbial Diseases , Osaka University , Suita , Japan
| | - Jiro Fujita
- b Department of Infectious, Respiratory, and Digestive Medicine, Graduate School of Medicine , University of the Ryukyus , Nakagami-gun , Japan
| | - Shota Nakamura
- a Department of Infection Metagenomics, Genome Information Research Center, Research Institute for Microbial Diseases , Osaka University , Suita , Japan.,c Laboratory of Pathogen Detection and Identification, International Research Center for Infectious Diseases, Research Institute for Microbial Diseases , Osaka University , Suita , Japan.,e Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives , Osaka University , Suita , Japan
| |
Collapse
|
38
|
Klann E, Beal SG, Tremblay EE. Evaluating differences in tuberculosis and nontuberculous mycobacterial lung disease in Florida. Am J Infect Control 2019; 47:1324-1328. [PMID: 31204093 DOI: 10.1016/j.ajic.2019.04.171] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 04/18/2019] [Accepted: 04/19/2019] [Indexed: 01/15/2023]
Abstract
BACKGROUND Currently, very little data exists that compare the features of pulmonary nontuberculous mycobacteria (NTM) and Mycobacterium tuberculosis (TB). Both have similar symptomology and analogous preliminary laboratory results, as both present with positive acid-fast bacilli stains. The objective of this study was to provide data that would help guide clinicians in their decision making regarding isolation precautions for patients, with a preliminary positive result for mycobacteria, prior to species identification. METHODS We conducted queries for patients who had positive respiratory cultures for mycobacteria via our electronic medical record system, between January 1, 2011, and December 31, 2017. Additionally, we collected demographic and medical history, clinical presentation, and radiographic findings. The 2-sample unpaired Student t test, the Χ2 test, and logistic regression were used to compare each group. RESULTS Through logistic regression, 8 variables were significantly associated with patients who grew either TB or NTM. History of incarceration, born outside of the United States, cavitation, and lymphadenopathy were associated with TB; tobacco smoke exposure, pre-existing lung disease, immunosuppression, and bronchiectasis were associated with NTM. Incidence of HIV and hemoptysis was not significantly different between the 2 groups. CONCLUSIONS Through the use of our study findings, improper use of airborne isolation precautions may be reduced or avoided.
Collapse
|
39
|
Revisiting John Snow to Meet the Challenge of Nontuberculous Mycobacterial Lung Disease. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:ijerph16214250. [PMID: 31683836 PMCID: PMC6862550 DOI: 10.3390/ijerph16214250] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 10/25/2019] [Accepted: 10/28/2019] [Indexed: 01/09/2023]
Abstract
Nontuberculous mycobacteria (NTM) are ubiquitous components of the soil and surface water microbiome. Disparities by sex, age, and geography demonstrate that both host and environmental factors are key determinants of NTM disease in populations, which predominates in the form of chronic pulmonary disease. As the incidence of NTM pulmonary disease rises across the United States, it becomes increasingly evident that addressing this emerging human health issue requires a bold, multi-disciplinary research framework that incorporates host risk factors for NTM pulmonary disease alongside the determinants of NTM residence in the environment. Such a framework should include the assessment of environmental characteristics promoting NTM growth in soil and surface water, detailed evaluations of water distribution systems, direct sampling of water sources for NTM contamination and species diversity, and studies of host and bacterial factors involved in NTM pathogenesis. This comprehensive approach can identify intervention points to interrupt the transmission of pathogenic NTM species from the environment to the susceptible host and to reduce NTM pulmonary disease incidence.
Collapse
|
40
|
Socio-Economic and Environmental Factors Related to Spatial Differences in Human Non-Tuberculous Mycobacterial Diseases in the Czech Republic. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:ijerph16203969. [PMID: 31627484 PMCID: PMC6843547 DOI: 10.3390/ijerph16203969] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 10/16/2019] [Indexed: 02/07/2023]
Abstract
Non-tuberculous mycobacteria (NTM) are ubiquitous environmental bacteria that can induce pulmonary and non-pulmonary diseases in susceptible persons. It is reported that the prevalence of NTM diseases is increasing in developed countries, but this differs by regions and countries. NTM species distribution and the rate of diseases caused by NTM vary widely in the historical territories of Moravia and Silesia (Czech Republic). This epidemiologic study of NTM diseases covers the period 2012–2018, reviews isolates obtained from patients with clinical disease and investigates correlations with related socio-economic and environmental factors. Individual NTM patients were included only once during the studied period and results were presented as incidence rate per year. The most frequently isolated NTM meeting the microbiological and clinical criteria in the study were the Mycobacterium avium-intracellulare complex, followed by Mycobacterium kansasii and Mycobacteriumxenopi. A previously described endemic incidence of M.kansasii in the Karviná district and M.xenopi in the Ostrava district was also observed in this study. The incidence of NTM patients in the whole studied territory was 1.10/100,000 inhabitants (1.33/100,000 in men and 0.88/100,000 in women). The annual incidence of lymphadenitis in children (≤5 years of age) was 2.35/100,000 of the population of children during the 7 year period but increased in the year 2018 to 5.95/100,000. The rate of human tuberculosis in the studied area was 1.97/100,000 inhabitants. The incidence of NTM pulmonary diseases correlated with a lower socio-economic status (r = 0.63) and a higher concentration of benzo[a]pyrene pollution in the air (r = 0.64).
Collapse
|
41
|
A Global Survey of Mycobacterial Diversity in Soil. Appl Environ Microbiol 2019; 85:AEM.01180-19. [PMID: 31253672 DOI: 10.1128/aem.01180-19] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 06/20/2019] [Indexed: 12/14/2022] Open
Abstract
Mycobacteria are a diverse bacterial group ubiquitous in many soil and aquatic environments. Members of this group have been associated with human and other animal diseases, including the nontuberculous mycobacteria (NTM), which are of growing relevance to public health worldwide. Although soils are often considered an important source of environmentally acquired NTM infections, the biodiversity and ecological preferences of soil mycobacteria remain largely unexplored across contrasting climates and ecosystem types. Using a culture-independent approach by combining 16S rRNA marker gene sequencing with mycobacterium-specific hsp65 gene sequencing, we analyzed the diversity, distributions, and environmental preferences of soil-dwelling mycobacteria in 143 soil samples collected from a broad range of ecosystem types. The surveyed soils harbored highly diverse mycobacterial communities that span the full extent of the known mycobacterial phylogeny, with most soil mycobacteria (97% of mycobacterial clades) belonging to previously undescribed lineages. While mycobacteria tended to have higher relative abundances in cool, wet, and acidic soil environments, several individual mycobacterial clades had contrasting environmental preferences. We identified the environmental preferences of many mycobacterial clades, including the clinically relevant Mycobacterium avium complex that was more commonly detected in wet and acidic soils. However, most of the soil mycobacteria detected were not closely related to known pathogens, calling into question previous assumptions about the general importance of soil as a source of NTM infections. Together, this work provides novel insights into the diversity, distributions, and ecological preferences of soil mycobacteria and lays the foundation for future efforts to link mycobacterial phenotypes to their distributions.IMPORTANCE Mycobacteria are common inhabitants of soil, and while most members of this bacterial group are innocuous, some mycobacteria can cause environmentally acquired infections of humans and other animals. Human infections from nontuberculous mycobacteria (NTM) are increasingly prevalent worldwide, and some areas appear to be "hotspots" for NTM disease. While exposure to soil is frequently implicated as an important mode of NTM transmission, the diversity, distributions, and ecological preferences of soil mycobacteria remain poorly understood. We analyzed 143 soils from a range of ecosystems and found that mycobacteria and lineages within the group often exhibited predictable preferences for specific environmental conditions. Soils harbor large amounts of previously undescribed mycobacterial diversity, and lineages that include known pathogens were rarely detected in soil. Together, these findings suggest that soil is an unlikely source of many mycobacterial infections. The biogeographical patterns we documented lend insight into the ecology of this important group of soil-dwelling bacteria.
Collapse
|
42
|
Zhou L, Ma C, Xiao T, Li M, Liu H, Zhao X, Wan K, Wang R. A New Single Gene Differential Biomarker for Mycobacterium tuberculosis Complex and Non-tuberculosis Mycobacteria. Front Microbiol 2019; 10:1887. [PMID: 31456790 PMCID: PMC6700215 DOI: 10.3389/fmicb.2019.01887] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 07/30/2019] [Indexed: 12/28/2022] Open
Abstract
Background Tuberculosis (TB) and non-tuberculous mycobacteriosis are serious threats to health worldwide. A simple non-sequencing method is needed for rapid diagnosis, especially in less experienced hospitals, but there is no specific biomarker commonly used for all mycobacteria. The ku gene of the prokaryotic error-prone non-homologous end joining system (NHEJ) has the potential to be a highly specific detection biomarker for mycobacteria. Methods A total of 7294 mycobacterial genomes and 14 complete genomes of other families belonging to Corynebacteriales with Mycobacteriaceae were downloaded and analyzed for the existence and variation of the ku gene. Mycobacterium tuberculosis complex (MTBC) and non-tuberculosis mycobacteria (NTM)- specific primers were designed and the actual amplification and identification efficiencies were tested with 150 strains of 40 Mycobacterium species and 10 kinds of common respiratory pathogenic bacteria. Results The ku gene of the NHEJ system was ubiquitous in all genome sequenced Mycobacterium species and absent in other families of Corynebacteriales. On the one hand, as a single gene non-sequencing biomarker, its specific primers could effectively distinguish mycobacteria from other bacteria, MTBC from NTM, which would make the clinical detection of mycobacteria easy and have great clinical practical value. On the other hand, the sequence of ku gene can effectively distinguish NTM to species level with high resolution. Conclusion The Ku protein existed before the differentiation of Mycobacterium species, which was an important protein involved in maintaining of the genome’s integrity and related to the special growth stage of mycobacteria. It was rare in prokaryotes. These features made it a highly special differential biomarker for Mycobacterium.
Collapse
Affiliation(s)
- Lei Zhou
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,College of Pharmacy, Guizhou University, Guiyang, China
| | - Cuidie Ma
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Tongyang Xiao
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Machao Li
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Haican Liu
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiuqin Zhao
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Kanglin Wan
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Ruibai Wang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| |
Collapse
|
43
|
Mycobacterium avium complex pulmonary disease: new epidemiology and management concepts. Curr Opin Infect Dis 2019; 31:199-207. [PMID: 29346118 DOI: 10.1097/qco.0000000000000437] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
PURPOSE OF REVIEW The prevalence of Mycobacterium avium complex (MAC)-related pulmonary disease has been increasing because of environmental factors, changes in organism virulence, and evolving host susceptibility. Treatment is often complicated by adverse effects, development of drug resistance, and refractory disease, with recurrence rates as high as 25-45%. RECENT FINDINGS Aerosolization of water, soil, or dusts are the likely sources of MAC-related pulmonary disease in susceptible individuals. The management of MAC-related pulmonary disease requires a multimodality approach, including antimicrobial therapy in appropriate patients, employment of mucus clearance techniques, instituting changes in the individual's home environment and personal habits to reduce environmental exposure to MAC, prevention of reflux, and maintenance of a healthy body weight. When the standard treatment for MAC-related pulmonary disease is not possible because of drug intolerance, antibiotic resistance, or progression of disease, second-line agents such as inhaled amikacin, clofazimine, bedaquiline, and delamanid must be considered, despite limited experience and few studies to guide their use. SUMMARY Individuals who have proven to be susceptible to MAC-related pulmonary disease should institute measures to reduce exposure to environmental sources of infection. Further research is needed to assess the impact of such preventive strategies on the incidence of new infection and disease recurrence. The efficacy of new medications for MAC-related pulmonary disease and their use in different combinations also requires further study.
Collapse
|
44
|
Keikha M. Comment on "A case of Mycobacterium chelonae mediastinitis and acute humoral rejection after heart transplantation". J Card Surg 2019; 34:647-648. [PMID: 31197871 DOI: 10.1111/jocs.14077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 04/07/2019] [Indexed: 02/05/2023]
Affiliation(s)
- Masoud Keikha
- Department of Microbiology and Virology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| |
Collapse
|
45
|
Sadeghi M, Kiani A, Sheikhy K, Taghavi K, Farrokhpour M, Abedini A. Abdominal Compartment Syndrome in Critically Ill Patients. Open Access Maced J Med Sci 2019; 7:1097-1102. [PMID: 31049088 PMCID: PMC6490480 DOI: 10.3889/oamjms.2019.228] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 04/03/2019] [Accepted: 04/04/2019] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Abdominal compartment syndrome patients suffer severe obstacles such as kidney failure and shock. To evade further complications, identifying the abdominal compartment syndrome (ACS) and Intra-abdominal hypertension (IAH), in critically ill individuals and hospitalised in the intensive care unit (ICU) is obligated. AIM The current study intended to study the abdominal compartment syndrome and the concomitant risk factors among hospitalised patients in ICU, by using the Intra-abdominal pressure test. MATERIAL AND METHODS One hundred and twenty-five hospitalised patients at ICU entered the current survey. Abdominal pressure was measured by standard intravesical technique. The SPSS 21 analysed the preoperative and intraoperative factors such as demographic records and comorbidities. RESULTS Seventy-three (58.4%) participants were males and 52 (41.6%) were women in the mean age of 55.1 ± 18.3 years. Eighty-nine patients (71.2%) showed normal intra-abdominal pressure since 31 patients (24.8%), and 5 patients (4%) developed IAH and ACS. The intra-abdominal pressure (IAP) applied to Glasgow Coma Scale (GCS), Acute Physiology, shock, Systemic Inflammatory Response Syndrome (SIRS), central venous oxygen saturation and Chronic Health Evaluation (APACHE II) score (P < 0.05). Patients with high IAP have shown a higher mortality frequency, compared to others (P < 0.05). CONCLUSION Current findings showed a correlation between IAP hospitalised patients in ICU and shock, SIRS, APACHE II, central venous oxygen saturation and GCS. Intra-abdominal pressure test, as a valuable prognosis test for the abdominal compartment syndrome (ACS) and Intra-abdominal hypertension (IAH), may offer better results when added to the routine medical checkup of ICU patients.
Collapse
Affiliation(s)
- Mohsen Sadeghi
- Chronic Respiratory Diseases Research Center, National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Arda Kiani
- Tracheal Diseases Research Center, National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Kambiz Sheikhy
- Lung Transplantation Research Center, National Research Institute of Tuberculosis and Lung Disease (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Kimia Taghavi
- Chronic Respiratory Diseases Research Center, National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohsen Farrokhpour
- Chronic Respiratory Diseases Research Center, National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Atefeh Abedini
- Chronic Respiratory Diseases Research Center, National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| |
Collapse
|
46
|
Jones RS, Shier KL, Master RN, Bao JR, Clark RB. Current significance of the Mycobacterium chelonae-abscessus group. Diagn Microbiol Infect Dis 2019; 94:248-254. [PMID: 30954313 DOI: 10.1016/j.diagmicrobio.2019.01.021] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 01/30/2019] [Accepted: 01/31/2019] [Indexed: 02/08/2023]
Abstract
Organisms of the Mycobacterium chelonae-abscessus group can be significant pathogens in humans. They produce a number of diseases including acute, invasive and chronic infections, which may be difficult to diagnose correctly. Identification among members of this group is complicated by differentiating at least eleven (11) known species and subspecies and complexity of identification methodologies. Treatment of their infections may be problematic due to their correct species identification, antibiotic resistance, their differential susceptibility to the limited number of drugs available, and scarcity of susceptibility testing.
Collapse
Affiliation(s)
- Robert S Jones
- Infectious Disease Department, Quest Diagnostics Nichols Institute, Chantilly, VA 20131
| | - Kileen L Shier
- Infectious Disease Department, Quest Diagnostics Nichols Institute, Chantilly, VA 20131
| | - Ronald N Master
- Infectious Disease Department, Quest Diagnostics Nichols Institute, Chantilly, VA 20131
| | - Jian R Bao
- Infectious Disease Department, Quest Diagnostics Nichols Institute, Chantilly, VA 20131
| | - Richard B Clark
- Infectious Disease Department, Quest Diagnostics Nichols Institute, Chantilly, VA 20131.
| |
Collapse
|
47
|
Carneiro MDS, Nunes LDS, David SMMD, Dias CF, Barth AL, Unis G. Nontuberculous mycobacterial lung disease in a high tuberculosis incidence setting in Brazil. ACTA ACUST UNITED AC 2019; 44:106-111. [PMID: 29791549 PMCID: PMC6044650 DOI: 10.1590/s1806-37562017000000213] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Accepted: 10/15/2017] [Indexed: 11/05/2022]
Abstract
Objective: The incidence of lung disease caused by nontuberculous mycobacteria (NTM) has been increasing worldwide. In Brazil, there are few studies about nontuberculous mycobacterial lung disease (NTMLD), and its prevalence is yet to be known. Our objective was to determine the specific etiology of the disease in the state of Rio Grande do Sul, Brazil, as well as the frequency and diversity of NTM species in our sample of patients. Methods: This is a retrospective analysis of the medical records of patients diagnosed with NTMLD treated in a referral center located in the city of Porto Alegre, Brazil, between 2003 and 2013. Results: Our sample comprised 100 patients. The most prevalent NTM species were Mycobacterium avium complex (MAC), in 35% of the cases; M. kansasii, in 17%; and M. abscessus, in 12%. A total of 85 patients had received previous treatment for tuberculosis. Associated conditions included structural abnormalities in the lungs, such as bronchiectasis, in 23% of the cases; COPD, in 17%; and immunosuppressive conditions, such as AIDS, in 24%. Conclusions: MAC and M. kansasii were the most prevalent species involved in NTMLD in the state, similarly to what occurs in other regions of Brazil. Data on regional epidemiology of NTMLD, its specific etiology, and associated conditions are essential to establish appropriate treatment, since each species requires specific regimens. Most patients with NTMLD had received previous tuberculosis treatment, which might lead to development of resistance and late diagnosis.
Collapse
Affiliation(s)
- Maiara Dos Santos Carneiro
- Programa de Pós-Graduação em Ciências Farmacêuticas, Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Luciana de Souza Nunes
- Laboratório de Pesquisa em Resistência Bacteriana, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brasil
| | | | | | - Afonso Luís Barth
- Programa de Pós-Graduação em Ciências Farmacêuticas, Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Gisela Unis
- Hospital Sanatório Partenon, Porto Alegre, RS, Brasil
| |
Collapse
|
48
|
Rana A, Thakur S, Kumar G, Akhter Y. Recent Trends in System-Scale Integrative Approaches for Discovering Protective Antigens Against Mycobacterial Pathogens. Front Genet 2018; 9:572. [PMID: 30538722 PMCID: PMC6277634 DOI: 10.3389/fgene.2018.00572] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 11/06/2018] [Indexed: 11/21/2022] Open
Abstract
Mycobacterial infections are one of the deadliest infectious diseases still posing a major health burden worldwide. The battle against these pathogens needs to focus on novel approaches and key interventions. In recent times, availability of genome scale data has revolutionized the fields of computational biology and immunoproteomics. Here, we summarize the cutting-edge ‘omics’ technologies and innovative system scale strategies exploited to mine the available data. These may be targeted using high-throughput technologies to expedite the identification of novel antigenic candidates for the rational next generation vaccines and serodiagnostic development against mycobacterial pathogens for which traditional methods have been failing.
Collapse
Affiliation(s)
- Aarti Rana
- School of Life Sciences, Central University of Himachal Pradesh, Shahpur, India
| | - Shweta Thakur
- School of Life Sciences, Central University of Himachal Pradesh, Shahpur, India
| | - Girish Kumar
- School of Life Sciences, Central University of Himachal Pradesh, Shahpur, India
| | - Yusuf Akhter
- Department of Biotechnology, Babasaheb Bhimrao Ambedkar University, Lucknow, India
| |
Collapse
|
49
|
Abstract
Bacteria thrive in showerheads and throughout household water distribution systems. While most of these bacteria are innocuous, some are potential pathogens, including members of the genus Mycobacterium that can cause nontuberculous mycobacterial (NTM) lung infection, an increasing threat to public health. We found that showerheads in households across the United States and Europe often harbor abundant mycobacterial communities that vary in composition depending on geographic location, water chemistry, and water source, with households receiving water treated with chlorine disinfectants having particularly high abundances of certain mycobacteria. The regions in the United States where NTM lung infections are most common were the same regions where pathogenic mycobacteria were most prevalent in showerheads, highlighting the important role of showerheads in the transmission of NTM infections. Bacteria within the genus Mycobacterium can be abundant in showerheads, and the inhalation of aerosolized mycobacteria while showering has been implicated as a mode of transmission in nontuberculous mycobacterial (NTM) lung infections. Despite their importance, the diversity, distributions, and environmental predictors of showerhead-associated mycobacteria remain largely unresolved. To address these knowledge gaps, we worked with citizen scientists to collect showerhead biofilm samples and associated water chemistry data from 656 households located across the United States and Europe. Our cultivation-independent analyses revealed that the genus Mycobacterium was consistently the most abundant genus of bacteria detected in residential showerheads, and yet mycobacterial diversity and abundances were highly variable. Mycobacteria were far more abundant, on average, in showerheads receiving municipal water than in those receiving well water and in U.S. households than in European households, patterns that are likely driven by differences in the use of chlorine disinfectants. Moreover, we found that water source, water chemistry, and household location also influenced the prevalence of specific mycobacterial lineages detected in showerheads. We identified geographic regions within the United States where showerheads have particularly high abundances of potentially pathogenic lineages of mycobacteria, and these “hot spots” generally overlapped those regions where NTM lung disease is most prevalent. Together, these results emphasize the public health relevance of mycobacteria in showerhead biofilms. They further demonstrate that mycobacterial distributions in showerhead biofilms are often predictable from household location and water chemistry, knowledge that advances our understanding of NTM transmission dynamics and the development of strategies to reduce exposures to these emerging pathogens.
Collapse
|
50
|
Rodríguez-Sevilla G, Rigauts C, Vandeplassche E, Ostyn L, Mahíllo-Fernández I, Esteban J, Peremarch CPJ, Coenye T, Crabbé A. Influence of three-dimensional lung epithelial cells and interspecies interactions on antibiotic efficacy against Mycobacterium abscessus and Pseudomonas aeruginosa. Pathog Dis 2018; 76:4966983. [PMID: 29648588 DOI: 10.1093/femspd/fty034] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Accepted: 04/09/2018] [Indexed: 12/26/2022] Open
Abstract
Mycobacterium abscessus lung infection is a major health problem for cystic fibrosis (CF) patients. Understanding the in vivo factors that influence the outcome of therapy may help addressing the poor correlation between in vitro and in vivo antibiotic efficacy. We evaluated the influence of interspecies interactions and lung epithelial cells on antibiotic efficacy. Therefore, single and dual-species biofilms of M. abscessus and a major CF pathogen (Pseudomonas aeruginosa) were cultured on a plastic surface or on in vivo-like three-dimensional (3-D) lung epithelial cells, and the activity of antibiotics (colistin, amikacin, clarithromycin, ceftazidime) in inhibiting biofilm formation was evaluated. Using the most physiologically relevant model (dual-species biofilms on 3-D cells), we observed that treatment with antibiotics during biofilm development inhibited P. aeruginosa but not M. abscessus biofilms, resulting in a competitive advantage for the latter. Clarithromycin efficacy against P. aeruginosa was inhibited by 3-D lung cells. In addition, biofilm induction of M. abscessus was observed by certain antibiotics on plastic but not on 3-D cells. Pseudomonas aeruginosa influenced the efficacy of certain antibiotics against M. abscessus, but not vice versa. In conclusion, these results suggest a role of host cells and interspecies interactions in bacterial responses to antimicrobials.
Collapse
Affiliation(s)
| | - Charlotte Rigauts
- Laboratory of Pharmaceutical Microbiology, Ghent University, B-9000 Ghent, Belgium
| | - Eva Vandeplassche
- Laboratory of Pharmaceutical Microbiology, Ghent University, B-9000 Ghent, Belgium
| | - Lisa Ostyn
- Laboratory of Pharmaceutical Microbiology, Ghent University, B-9000 Ghent, Belgium
| | | | - Jaime Esteban
- Department of Clinical Microbiology, IIS- Fundación Jiménez Díaz, UAM, Madrid, 28040 Madrid, Spain
| | | | - Tom Coenye
- Laboratory of Pharmaceutical Microbiology, Ghent University, B-9000 Ghent, Belgium
| | - Aurélie Crabbé
- Laboratory of Pharmaceutical Microbiology, Ghent University, B-9000 Ghent, Belgium
| |
Collapse
|