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Turchi B, Campobasso C, Nardinocchi A, Wagemans J, Torracca B, Lood C, Di Giuseppe G, Nieri P, Bertelloni F, Turini L, Ruffo V, Lavigne R, Di Luca M. Isolation and characterization of novel Staphylococcus aureus bacteriophage Hesat from dairy origin. Appl Microbiol Biotechnol 2024; 108:299. [PMID: 38619619 PMCID: PMC11018700 DOI: 10.1007/s00253-024-13129-y] [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: 09/05/2023] [Revised: 03/05/2024] [Accepted: 03/27/2024] [Indexed: 04/16/2024]
Abstract
A novel temperate phage, named Hesat, was isolated by the incubation of a dairy strain of Staphylococcus aureus belonging to spa-type t127 with either bovine or ovine milk. Hesat represents a new species of temperate phage within the Phietavirus genus of the Azeredovirinae subfamily. Its genome has a length of 43,129 bp and a GC content of 35.11% and contains 75 predicted ORFs, some of which linked to virulence. This includes (i) a pathogenicity island (SaPln2), homologous to the type II toxin-antitoxin system PemK/MazF family toxin; (ii) a DUF3113 protein (gp30) that is putatively involved in the derepression of the global repressor Stl; and (iii) a cluster coding for a PVL. Genomic analysis of the host strain indicates Hesat is a resident prophage. Interestingly, its induction was obtained by exposing the bacterium to milk, while the conventional mitomycin C-based approach failed. The host range of phage Hesat appears to be broad, as it was able to lyse 24 out of 30 tested S. aureus isolates. Furthermore, when tested at high titer (108 PFU/ml), Hesat phage was also able to lyse a Staphylococcus muscae isolate, a coagulase-negative staphylococcal strain. KEY POINTS: • A new phage species was isolated from a Staphylococcus aureus bovine strain. • Pathogenicity island and PVL genes are encoded within phage genome. • The phage is active against most of S. aureus strains from both animal and human origins.
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Affiliation(s)
- Barbara Turchi
- Department of Veterinary Sciences, University of Pisa, Viale Delle Piagge 2, 56124, Pisa, Italy
| | - Claudia Campobasso
- Department of Biology, University of Pisa, Via San Zeno 37, 56127, Pisa, Italy
- Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21, Box 2462, 3001, Louvain, Belgium
| | - Arianna Nardinocchi
- Department of Biology, University of Pisa, Via San Zeno 37, 56127, Pisa, Italy
| | - Jeroen Wagemans
- Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21, Box 2462, 3001, Louvain, Belgium
| | - Beatrice Torracca
- Department of Veterinary Sciences, University of Pisa, Viale Delle Piagge 2, 56124, Pisa, Italy
| | - Cédric Lood
- Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21, Box 2462, 3001, Louvain, Belgium
- Department of Microbial and Molecular Systems, Centre for Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, Box 2460, 3001, Leuven, Belgium
| | | | - Paola Nieri
- Department of Pharmacy, University of Pisa, Via Bonanno Pisano 6, 56126, Pisa, Italy
| | - Fabrizio Bertelloni
- Department of Veterinary Sciences, University of Pisa, Viale Delle Piagge 2, 56124, Pisa, Italy
| | - Luca Turini
- Department of Veterinary Sciences, University of Pisa, Viale Delle Piagge 2, 56124, Pisa, Italy
| | - Valeria Ruffo
- Department of Veterinary Sciences, University of Pisa, Viale Delle Piagge 2, 56124, Pisa, Italy
| | - Rob Lavigne
- Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21, Box 2462, 3001, Louvain, Belgium
| | - Mariagrazia Di Luca
- Department of Biology, University of Pisa, Via San Zeno 37, 56127, Pisa, Italy.
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Xiao J, Huang J, Xue X, Wang C, Sun Y, Zheng L, Zhao X, Wang X, Zhao X, Xue H. Novel cassette chromosome recombinases CcrA8B9 catalyse the excision and integration of the staphylococcal cassette chromosome mec element. J Antimicrob Chemother 2023; 78:440-444. [PMID: 36480296 DOI: 10.1093/jac/dkac410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Accepted: 11/15/2022] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVES A defining feature of MRSA is the SCCmec element. The excision and integration of SCCmec elements are catalysed by Ccr recombinases. Currently, seven ccrA, eight ccrB and two ccrC allotypes have been described. However, there have been no recent reports of a novel Ccr recombinase and thus this area should be explored. METHODS According to the proposed criteria of the International Working Group on the Classification of Staphylococcal Cassette Chromosome Elements (IWG-SCC) committee, novel ccr genes were explored by searching the genome of our laboratory staphylococcal strains, which were isolated from bovine mastitis in Northwest China. The biological activity of the novel Ccr recombinases to excise and integrate SCCmec elements was determined. The distribution of the novel ccr genes in staphylococci was conducted by querying the NCBI nr/nt database. RESULTS We report a set of novel Ccr recombinases CcrA8B9, which share nucleotide identities of 46.6%-50.2% and 47.4%-52.8% with the ccrA and ccrB alleles, respectively. We used PCR to show that CcrA8B9 can excise and integrate the SCCmec element. Furthermore, using NCBI BLAST we showed that the ccrA8B9 genes exist in other staphylococcal strains. Unlike the common ccr genes, ccrA8B9 is located outside the SCCmec/SCC element. CONCLUSIONS The novel Ccr recombinases CcrA8B9 can help excise and integrate SCCmec/SCC from the genome and provide a new way to facilitate the transmission of SCCmec/SCC elements among staphylococci.
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Affiliation(s)
- Jinhe Xiao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Jianguo Huang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Xuemei Xue
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Chen Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Yanting Sun
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Liangjun Zheng
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Xu Zhao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Xiaokun Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Xin Zhao
- Department of Animal Science, McGill University, Sainte-Anne-de-Bellevue, Quebec, Canada
| | - Huping Xue
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
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Molecular Epidemiology, Antimicrobial Susceptibility, and Clinical Features of Methicillin-Resistant Staphylococcus aureus Bloodstream Infections over 30 Years in Barcelona, Spain (1990-2019). Microorganisms 2022; 10:microorganisms10122401. [PMID: 36557654 PMCID: PMC9788191 DOI: 10.3390/microorganisms10122401] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 11/28/2022] [Accepted: 12/01/2022] [Indexed: 12/11/2022] Open
Abstract
Methicillin-resistant Staphylococcus aureus bloodstream infections (MRSA-BSI) are a significant cause of mortality. We analysed the evolution of the molecular and clinical epidemiology of MRSA-BSI (n = 784) in adult patients (Barcelona, 1990−2019). Isolates were tested for antimicrobial susceptibility and genotyped (PFGE), and a selection was sequenced (WGS) to characterise the pangenome and mechanisms underlying antimicrobial resistance. Increases in patient age (60 to 71 years), comorbidities (Charlson’s index > 2, 10% to 94%), community-onset healthcare-associated acquisition (9% to 60%), and 30-day mortality (28% to 36%) were observed during the 1990−1995 and 2014−2019 periods. The proportion of catheter-related BSIs fell from 57% to 20%. Current MRSA-BSIs are caused by CC5-IV and an upward trend of CC8-IV and CC22-IV clones. CC5 and CC8 had the lowest core genome proportions. Antimicrobial resistance rates fell, and only ciprofloxacin, tobramycin, and erythromycin remained high (>50%) due to GyrA/GrlA changes, the presence of aminoglycoside-modifying enzymes (AAC(6′)-Ie-APH(2″)-Ia and ANT(4′)-Ia), and mph(C)/msr(A) or erm (C) genes. Two CC22-IV strains showed daptomycin resistance (MprF substitutions). MRSA-BSI has become healthcare-associated, affecting elderly patients with comorbidities and causing high mortality rates. Clonal replacement with CC5-IV and CC8-IV clones resulted in lower antimicrobial resistance rates. The increased frequency of the successful CC22-IV, associated with daptomycin resistance, should be monitored.
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Abstract
Staphylococcus aureus causes a variety of debilitating and life-threatening diseases, and thus remains a challenging global health threat. S. aureus is remarkably diverse, yet only a minority of methicillin-resistant S. aureus (MRSA) clones have caused pandemic proportions of diseases. The genetic drivers of the successful dissemination of some clones across wide geographical expanses remain poorly understood. We analyzed 386 recently published MRSA genomes from bloodstream infections sampled in North, Central, and South America from 2011 to 2018. Here, we show that MRSA-associated bloodstream infections were attributable to two genetically distinct lineages. One lineage consisted almost exclusively of sequence type (ST) 8, which emerged in 1964. A second lineage emerged in 1986 and consisted of STs 5, 105, and 231. The two lineages have simultaneously disseminated across geographically distant sites. Sublineages rapidly diverged within locations in the early 2000s. Their diversification was associated with independent acquisitions of unique variants of the mobile mecA-carrying chromosomal cassette and distinct repertoires of antimicrobial resistance genes. We show that the evolution and spread of invasive multidrug-resistant MRSA in the Americas was driven by transcontinental dissemination, followed by more recent establishment and divergence of local pathogen populations. Our study highlights the need for continued international surveillance of high-risk clones to control the global health threat of multidrug resistance. IMPORTANCE Bloodstream infections due to S. aureus cause significant patient morbidity and mortality worldwide, exacerbated by the emergence and spread of methicillin resistant S. aureus (MRSA). This study provides important insights on the evolution and long-distance geographic expansion of two distinct MRSA lineages that predominate in bloodstream infections in the past 5 decades. The success of these two lineages partly lies on their acquisition of a diverse set of antimicrobial resistance genes and of unique variants of the mobile genetic element SCCmec that carries the gene mecA conferring resistance to beta-lactams. High-risk antimicrobial resistant clones can therefore rapidly disseminate across long distances and establish within local communities within a short period of time. These results have important implications for global initiatives and local epidemiological efforts to monitor and control invasive MRSA infections and transcontinental spread of multidrug resistance.
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Sundermann AJ, Chen J, Miller JK, Martin EM, Snyder GM, Van Tyne D, Marsh JW, Dubrawski A, Harrison LH. Whole-genome sequencing surveillance and machine learning for healthcare outbreak detection and investigation: A systematic review and summary. ANTIMICROBIAL STEWARDSHIP & HEALTHCARE EPIDEMIOLOGY : ASHE 2022; 2:e91. [PMID: 36483409 PMCID: PMC9726481 DOI: 10.1017/ash.2021.241] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 11/04/2021] [Indexed: 06/17/2023]
Abstract
BACKGROUND Whole-genome sequencing (WGS) has traditionally been used in infection prevention to confirm or refute the presence of an outbreak after it has occurred. Due to decreasing costs of WGS, an increasing number of institutions have been utilizing WGS-based surveillance. Additionally, machine learning or statistical modeling to supplement infection prevention practice have also been used. We systematically reviewed the use of WGS surveillance and machine learning to detect and investigate outbreaks in healthcare settings. METHODS We performed a PubMed search using separate terms for WGS surveillance and/or machine-learning technologies for infection prevention through March 15, 2021. RESULTS Of 767 studies returned using the WGS search terms, 42 articles were included for review. Only 2 studies (4.8%) were performed in real time, and 39 (92.9%) studied only 1 pathogen. Nearly all studies (n = 41, 97.6%) found genetic relatedness between some isolates collected. Across all studies, 525 outbreaks were detected among 2,837 related isolates (average, 5.4 isolates per outbreak). Also, 35 studies (83.3%) only utilized geotemporal clustering to identify outbreak transmission routes. Of 21 studies identified using the machine-learning search terms, 4 were included for review. In each study, machine learning aided outbreak investigations by complementing methods to gather epidemiologic data and automating identification of transmission pathways. CONCLUSIONS WGS surveillance is an emerging method that can enhance outbreak detection. Machine learning has the potential to identify novel routes of pathogen transmission. Broader incorporation of WGS surveillance into infection prevention practice has the potential to transform the detection and control of healthcare outbreaks.
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Affiliation(s)
- Alexander J. Sundermann
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Jieshi Chen
- Auton Lab, Carnegie Mellon University, Pittsburgh, Pennsylvania
| | - James K. Miller
- Auton Lab, Carnegie Mellon University, Pittsburgh, Pennsylvania
| | - Elise M. Martin
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- Department of Infection Prevention and Hospital Epidemiology, UPMC Presbyterian, Pittsburgh, Pennsylvania
| | - Graham M. Snyder
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- Department of Infection Prevention and Hospital Epidemiology, UPMC Presbyterian, Pittsburgh, Pennsylvania
| | - Daria Van Tyne
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Jane W. Marsh
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Artur Dubrawski
- Auton Lab, Carnegie Mellon University, Pittsburgh, Pennsylvania
| | - Lee H. Harrison
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania
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Prolonged outbreak of clonal, mupirocin-resistant methicillin-resistant Staphylococcus aureus in a neonatal intensive care unit: association with personnel and a possible environmental reservoir, analyzed using whole genome sequencing. Am J Infect Control 2022; 50:680-685. [PMID: 34543708 DOI: 10.1016/j.ajic.2021.09.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 09/10/2021] [Accepted: 09/11/2021] [Indexed: 11/20/2022]
Abstract
BACKGROUND Outbreaks of MRSA occur in NICUs and may be difficult to control. We describe an outbreak of mupirocin-resistant MRSA, molecular epidemiology of isolates and control. METHODS Medical record review of personnel contact with infants. MRSA isolates were analyzed by whole genome sequencing (WGS); single nucleotide polymorphisms (SNPs) were identified. RESULTS A 31-month outbreak of MRSA infection occurred. Weekly colonization surveillance of infants was initiated; initial prevalence was 45%. Isolates exhibited high level mupirocin-resistance. There were 3 periods of increased colonization and new infections despite implementation of multiple infection prevention interventions. During the second period, an analysis identified a frontline staff member associated with newly colonized infants whose nasal culture grew the clonal MRSA. A marked reduction in colonization followed removal from patient contact. WGS of isolates from years 1-3 showed clonality with maximum SNP differences of 33. Importantly, the year 3 isolates were more closely related to the early year 1 isolates (15-20 SNP differences) than to the late year 1 or year 2 isolates (18-33 SNP differences). DISCUSSION/CONCLUSIONS During a recrudescent MRSA outbreak due to a clonal strain, both contact with a colonized staff member and a putative environmental or personnel reservoir were associated with MRSA acquisition.
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Greninger AL, Zerr DM. NGSocomial Infections: High-Resolution Views of Hospital-Acquired Infections Through Genomic Epidemiology. J Pediatric Infect Dis Soc 2021; 10:S88-S95. [PMID: 34951469 PMCID: PMC8755322 DOI: 10.1093/jpids/piab074] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Hospital outbreak investigations are high-stakes epidemiology. Contacts between staff and patients are numerous; environmental and community exposures are plentiful; and patients are highly vulnerable. Having the best data is paramount to understanding an outbreak in order to stop ongoing transmission and prevent future outbreaks. In the past 5 years, the high-resolution view of transmission offered by analyzing pathogen whole-genome sequencing (WGS) is increasingly part of hospital outbreak investigations. Concerns over speed and actionability, assay validation, liability, cost, and payment models lead to further opportunities for work in this area. Now accelerated by funding for COVID-19, the use of genomics in hospital outbreak investigations has firmly moved from the academic literature to more quotidian operations, with associated concerns involving regulatory affairs, data integration, and clinical interpretation. This review details past uses of WGS data in hospital-acquired infection outbreaks as well as future opportunities to increase its utility and growth in hospital infection prevention.
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Affiliation(s)
- Alexander L Greninger
- Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, Washington, USA,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA,Corresponding Author: Alexander L. Greninger MD, PhD, MS, MPhil, 1616 Eastlake Ave East Suite 320, Seattle, WA 98102, USA. E-mail:
| | - Danielle M Zerr
- Department of Pediatrics, University of Washington Medical Center, Seattle, Washington, USA,Division of Infectious Diseases, Seattle Children’s Hospital, Seattle, Washington, USA
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Gitman MR, Alburquerque B, Chung M, van de Guchte A, Sullivan MJ, Obla A, Polanco J, Oussenko I, Smith ML, Samaroo F, Barackman D, Altman DR, Sordillo EM, van Bakel H. Modified methicillin-resistant Staphylococcus aureus detected in neonatal intensive care patients. J Antimicrob Chemother 2021; 76:2774-2777. [PMID: 34368846 PMCID: PMC8521402 DOI: 10.1093/jac/dkab266] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 06/29/2021] [Indexed: 11/16/2022] Open
Abstract
Objectives As part of an active MRSA surveillance programme in our neonatal ICU, we identified nares surveillance cultures from two infants that displayed heterogeneity in methicillin resistance between isolated subclones that lacked mecA and mecC. Methods The underlying mechanism for the modified Staphylococcus aureus (MODSA) methicillin-resistance phenotype was investigated by WGS. Results Comparison of finished-quality genomes of four MODSA and four MSSA subclones demonstrated that the resistance changes were associated with unique truncating mutations in the gene encoding the cyclic diadenosine monophosphate phosphodiesterase enzyme GdpP or a non-synonymous substitution in the gene encoding PBP2. Conclusions These two cases highlight the difficulty in identifying non-mecA, non-mecC-mediated MRSA isolates in the clinical microbiology laboratory, which leads to difficulties in implementing appropriate therapy and infection control measures.
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Affiliation(s)
- Melissa R Gitman
- Department of Pathology and Laboratory Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Bremy Alburquerque
- Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY, USA.,The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Marilyn Chung
- Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Adriana van de Guchte
- Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Mitchell J Sullivan
- Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Ajay Obla
- Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Jose Polanco
- Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Irina Oussenko
- Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Melissa L Smith
- Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Flora Samaroo
- Department of Pathology and Laboratory Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Debbie Barackman
- Department of Pathology and Laboratory Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Deena R Altman
- Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY, USA.,Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Emilia Mia Sordillo
- Department of Pathology and Laboratory Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Harm van Bakel
- Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
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Lee SE, Mushtaq A, Gitman M, Paniz-Mondolfi A, Chung M, Obla A, Sordillo EM, Nowak MD, van Bakel H, Ramírez JD, Muñoz M, Lee M. Lemierre's syndrome associated with hypervirulent Klebsiella pneumoniae: A case report and genomic characterization of the isolate. IDCases 2021; 25:e01173. [PMID: 34141583 PMCID: PMC8188389 DOI: 10.1016/j.idcr.2021.e01173] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 05/25/2021] [Accepted: 05/27/2021] [Indexed: 11/24/2022] Open
Abstract
We describe a case of Lemierre’s syndrome (LS) caused by a hypervirulent strain of Klebsiella pneumoniae in a 63-year-old female with hypertension, hyperlipidemia, and diabetes mellitus, who presented with right neck pain and fevers. Computerized tomography of the neck and chest revealed an occluded right internal jugular vein secondary to thrombosis and septic emboli in lungs. Blood cultures grew K. pneumoniae. The patient was treated with ampicillin-sulbactam and then transitioned to amoxicillin-clavulanate to complete a 6-week course of antibiotics, and a 3-month course of rivaroxaban. String test of the K. pneumoniae isolate was positive at 2 cm. Whole genome sequencing identified several genes associated with the hypervirulent strain, notably the genes encoding for aerobactin (iucA and iucB) and salmochelin (iroB) iron acquisition systems. LS can rarely be caused by K. pneumoniae. Clinicians should monitor for known complications, such as septic emboli in patients with LS.
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Affiliation(s)
- Seung Eun Lee
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ammara Mushtaq
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Melissa Gitman
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alberto Paniz-Mondolfi
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Marilyn Chung
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ajay Obla
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Emilia M Sordillo
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Michael D Nowak
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Harm van Bakel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Juan David Ramírez
- Centro de Investigaciones en Microbiología y Biotecnología -UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Marina Muñoz
- Centro de Investigaciones en Microbiología y Biotecnología -UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Mikyung Lee
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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10
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Viana AS, Nunes Botelho AM, Moustafa AM, Boge CL, Pires Ferreira AL, da Silva Carvalho MC, Guimarães MA, Costa BDSS, de Mattos MC, Maciel SP, Echevarria-Lima J, Narechania A, O’Brien K, Ryan C, Gerber JS, Carvalho BTF, Figueiredo AMS, Planet PJ. Multidrug-Resistant Methicillin-Resistant Staphylococcus aureus Associated with Bacteremia and Monocyte Evasion, Rio de Janeiro, Brazil. Emerg Infect Dis 2021; 27:2825-2835. [PMID: 34670645 PMCID: PMC8544994 DOI: 10.3201/eid2711.210097] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We typed 600 methicillin-resistant Staphylococcus aureus (MRSA) isolates collected in 51 hospitals in the Rio de Janeiro, Brazil, metropolitan area during 2014-2017. We found that multiple new clonal complex (CC) 5 sequence types had replaced previously dominant MRSA lineages in hospitals. Whole-genome analysis of 208 isolates revealed an emerging sublineage of multidrug-resistant MRSA, sequence type 105, staphylococcal cassette chromosome mec II, spa t002, which we designated the Rio de Janeiro (RdJ) clone. Using molecular clock analysis, we hypothesized that this lineage began to expand in the Rio de Janeiro metropolitan area in 2009. Multivariate analysis supported an association between bloodstream infections and the CC5 lineage that includes the RdJ clone. Compared with other closely related isolates, representative isolates of the RdJ clone more effectively evaded immune function related to monocytic cells, as evidenced by decreased phagocytosis rate and increased numbers of viable unphagocytosed (free) bacteria after in vitro exposure to monocytes.
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Affiliation(s)
| | | | | | - Craig L.K. Boge
- Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil (A.S. Viana, A.M.N. Botelho, A.L.P. Ferreira, M.C.S. Carvalho, M.A. Guimarães, B.S.S. Costa, M.C. Mattos, S.P. Maciel, J. Echevarria-Lima, B.T.F. Carvalho, A.M.S. Figueiredo)
- Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA (A.M. Moustafa, C.L.K. Boge, K. O’Brien, C. Ryan, J.S. Gerber, P.J. Planet)
- Diagnósticos da América S.A., Duque de Caxias, Brazil (A.L.P. Ferreira)
- American Museum of Natural History, New York, New York, USA (A. Narechania, P.J. Planet)
- University of Pennsylvania, Philadelphia (J.S. Gerber, P.J. Planet)
| | - Adriana Lucia Pires Ferreira
- Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil (A.S. Viana, A.M.N. Botelho, A.L.P. Ferreira, M.C.S. Carvalho, M.A. Guimarães, B.S.S. Costa, M.C. Mattos, S.P. Maciel, J. Echevarria-Lima, B.T.F. Carvalho, A.M.S. Figueiredo)
- Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA (A.M. Moustafa, C.L.K. Boge, K. O’Brien, C. Ryan, J.S. Gerber, P.J. Planet)
- Diagnósticos da América S.A., Duque de Caxias, Brazil (A.L.P. Ferreira)
- American Museum of Natural History, New York, New York, USA (A. Narechania, P.J. Planet)
- University of Pennsylvania, Philadelphia (J.S. Gerber, P.J. Planet)
| | - Maria Cícera da Silva Carvalho
- Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil (A.S. Viana, A.M.N. Botelho, A.L.P. Ferreira, M.C.S. Carvalho, M.A. Guimarães, B.S.S. Costa, M.C. Mattos, S.P. Maciel, J. Echevarria-Lima, B.T.F. Carvalho, A.M.S. Figueiredo)
- Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA (A.M. Moustafa, C.L.K. Boge, K. O’Brien, C. Ryan, J.S. Gerber, P.J. Planet)
- Diagnósticos da América S.A., Duque de Caxias, Brazil (A.L.P. Ferreira)
- American Museum of Natural History, New York, New York, USA (A. Narechania, P.J. Planet)
- University of Pennsylvania, Philadelphia (J.S. Gerber, P.J. Planet)
| | - Márcia Aparecida Guimarães
- Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil (A.S. Viana, A.M.N. Botelho, A.L.P. Ferreira, M.C.S. Carvalho, M.A. Guimarães, B.S.S. Costa, M.C. Mattos, S.P. Maciel, J. Echevarria-Lima, B.T.F. Carvalho, A.M.S. Figueiredo)
- Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA (A.M. Moustafa, C.L.K. Boge, K. O’Brien, C. Ryan, J.S. Gerber, P.J. Planet)
- Diagnósticos da América S.A., Duque de Caxias, Brazil (A.L.P. Ferreira)
- American Museum of Natural History, New York, New York, USA (A. Narechania, P.J. Planet)
- University of Pennsylvania, Philadelphia (J.S. Gerber, P.J. Planet)
| | | | - Marcos Corrêa de Mattos
- Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil (A.S. Viana, A.M.N. Botelho, A.L.P. Ferreira, M.C.S. Carvalho, M.A. Guimarães, B.S.S. Costa, M.C. Mattos, S.P. Maciel, J. Echevarria-Lima, B.T.F. Carvalho, A.M.S. Figueiredo)
- Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA (A.M. Moustafa, C.L.K. Boge, K. O’Brien, C. Ryan, J.S. Gerber, P.J. Planet)
- Diagnósticos da América S.A., Duque de Caxias, Brazil (A.L.P. Ferreira)
- American Museum of Natural History, New York, New York, USA (A. Narechania, P.J. Planet)
- University of Pennsylvania, Philadelphia (J.S. Gerber, P.J. Planet)
| | - Sabrina Pires Maciel
- Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil (A.S. Viana, A.M.N. Botelho, A.L.P. Ferreira, M.C.S. Carvalho, M.A. Guimarães, B.S.S. Costa, M.C. Mattos, S.P. Maciel, J. Echevarria-Lima, B.T.F. Carvalho, A.M.S. Figueiredo)
- Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA (A.M. Moustafa, C.L.K. Boge, K. O’Brien, C. Ryan, J.S. Gerber, P.J. Planet)
- Diagnósticos da América S.A., Duque de Caxias, Brazil (A.L.P. Ferreira)
- American Museum of Natural History, New York, New York, USA (A. Narechania, P.J. Planet)
- University of Pennsylvania, Philadelphia (J.S. Gerber, P.J. Planet)
| | - Juliana Echevarria-Lima
- Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil (A.S. Viana, A.M.N. Botelho, A.L.P. Ferreira, M.C.S. Carvalho, M.A. Guimarães, B.S.S. Costa, M.C. Mattos, S.P. Maciel, J. Echevarria-Lima, B.T.F. Carvalho, A.M.S. Figueiredo)
- Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA (A.M. Moustafa, C.L.K. Boge, K. O’Brien, C. Ryan, J.S. Gerber, P.J. Planet)
- Diagnósticos da América S.A., Duque de Caxias, Brazil (A.L.P. Ferreira)
- American Museum of Natural History, New York, New York, USA (A. Narechania, P.J. Planet)
- University of Pennsylvania, Philadelphia (J.S. Gerber, P.J. Planet)
| | - Apurva Narechania
- Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil (A.S. Viana, A.M.N. Botelho, A.L.P. Ferreira, M.C.S. Carvalho, M.A. Guimarães, B.S.S. Costa, M.C. Mattos, S.P. Maciel, J. Echevarria-Lima, B.T.F. Carvalho, A.M.S. Figueiredo)
- Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA (A.M. Moustafa, C.L.K. Boge, K. O’Brien, C. Ryan, J.S. Gerber, P.J. Planet)
- Diagnósticos da América S.A., Duque de Caxias, Brazil (A.L.P. Ferreira)
- American Museum of Natural History, New York, New York, USA (A. Narechania, P.J. Planet)
- University of Pennsylvania, Philadelphia (J.S. Gerber, P.J. Planet)
| | - Kelsey O’Brien
- Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil (A.S. Viana, A.M.N. Botelho, A.L.P. Ferreira, M.C.S. Carvalho, M.A. Guimarães, B.S.S. Costa, M.C. Mattos, S.P. Maciel, J. Echevarria-Lima, B.T.F. Carvalho, A.M.S. Figueiredo)
- Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA (A.M. Moustafa, C.L.K. Boge, K. O’Brien, C. Ryan, J.S. Gerber, P.J. Planet)
- Diagnósticos da América S.A., Duque de Caxias, Brazil (A.L.P. Ferreira)
- American Museum of Natural History, New York, New York, USA (A. Narechania, P.J. Planet)
- University of Pennsylvania, Philadelphia (J.S. Gerber, P.J. Planet)
| | - Chanelle Ryan
- Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil (A.S. Viana, A.M.N. Botelho, A.L.P. Ferreira, M.C.S. Carvalho, M.A. Guimarães, B.S.S. Costa, M.C. Mattos, S.P. Maciel, J. Echevarria-Lima, B.T.F. Carvalho, A.M.S. Figueiredo)
- Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA (A.M. Moustafa, C.L.K. Boge, K. O’Brien, C. Ryan, J.S. Gerber, P.J. Planet)
- Diagnósticos da América S.A., Duque de Caxias, Brazil (A.L.P. Ferreira)
- American Museum of Natural History, New York, New York, USA (A. Narechania, P.J. Planet)
- University of Pennsylvania, Philadelphia (J.S. Gerber, P.J. Planet)
| | - Jeffrey S. Gerber
- Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil (A.S. Viana, A.M.N. Botelho, A.L.P. Ferreira, M.C.S. Carvalho, M.A. Guimarães, B.S.S. Costa, M.C. Mattos, S.P. Maciel, J. Echevarria-Lima, B.T.F. Carvalho, A.M.S. Figueiredo)
- Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA (A.M. Moustafa, C.L.K. Boge, K. O’Brien, C. Ryan, J.S. Gerber, P.J. Planet)
- Diagnósticos da América S.A., Duque de Caxias, Brazil (A.L.P. Ferreira)
- American Museum of Natural History, New York, New York, USA (A. Narechania, P.J. Planet)
- University of Pennsylvania, Philadelphia (J.S. Gerber, P.J. Planet)
| | - Bernadete Teixeira Ferreira Carvalho
- Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil (A.S. Viana, A.M.N. Botelho, A.L.P. Ferreira, M.C.S. Carvalho, M.A. Guimarães, B.S.S. Costa, M.C. Mattos, S.P. Maciel, J. Echevarria-Lima, B.T.F. Carvalho, A.M.S. Figueiredo)
- Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA (A.M. Moustafa, C.L.K. Boge, K. O’Brien, C. Ryan, J.S. Gerber, P.J. Planet)
- Diagnósticos da América S.A., Duque de Caxias, Brazil (A.L.P. Ferreira)
- American Museum of Natural History, New York, New York, USA (A. Narechania, P.J. Planet)
- University of Pennsylvania, Philadelphia (J.S. Gerber, P.J. Planet)
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11
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Berbel Caban A, Pak TR, Obla A, Dupper AC, Chacko KI, Fox L, Mills A, Ciferri B, Oussenko I, Beckford C, Chung M, Sebra R, Smith M, Conolly S, Patel G, Kasarskis A, Sullivan MJ, Altman DR, van Bakel H. PathoSPOT genomic epidemiology reveals under-the-radar nosocomial outbreaks. Genome Med 2020; 12:96. [PMID: 33198787 PMCID: PMC7670629 DOI: 10.1186/s13073-020-00798-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 11/02/2020] [Indexed: 12/14/2022] Open
Abstract
Background Whole-genome sequencing (WGS) is increasingly used to map the spread of bacterial and viral pathogens in nosocomial settings. A limiting factor for more widespread adoption of WGS for hospital infection prevention practices is the availability of standardized tools for genomic epidemiology. Methods We developed the Pathogen Sequencing Phylogenomic Outbreak Toolkit (PathoSPOT) to automate integration of genomic and medical record data for rapid detection and tracing of nosocomial outbreaks. To demonstrate its capabilities, we applied PathoSPOT to complete genome surveillance data of 197 MRSA bacteremia cases from two hospitals during a 2-year period. Results PathoSPOT identified 8 clonal clusters encompassing 33 patients (16.8% of cases), none of which had been recognized by standard practices. The largest cluster corresponded to a prolonged outbreak of a hospital-associated MRSA clone among 16 adults, spanning 9 wards over a period of 21 months. Analysis of precise timeline and location data with our toolkit suggested that an initial exposure event in a single ward led to infection and long-term colonization of multiple patients, followed by transmissions to other patients during recurrent hospitalizations. Conclusions We demonstrate that PathoSPOT genomic surveillance enables the detection of complex transmission chains that are not readily apparent from epidemiological data and that contribute significantly to morbidity and mortality, enabling more effective intervention strategies.
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Affiliation(s)
- Ana Berbel Caban
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Theodore R Pak
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Ajay Obla
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Amy C Dupper
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Kieran I Chacko
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Lindsey Fox
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Alexandra Mills
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Brianne Ciferri
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Irina Oussenko
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Colleen Beckford
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Marilyn Chung
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY, USA.,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Sema4, a Mount Sinai venture, Stamford, CT, 06902, USA
| | - Melissa Smith
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY, USA.,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Sarah Conolly
- Infection Prevention, The Mount Sinai Hospital, New York City, NY, USA
| | - Gopi Patel
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York City, NY, USA.,Infection Prevention, The Mount Sinai Hospital, New York City, NY, USA
| | - Andrew Kasarskis
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY, USA.,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Mitchell J Sullivan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Deena R Altman
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York City, NY, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Harm van Bakel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY, USA. .,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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12
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Reva ON, Korotetskiy IS, Joubert M, Shilov SV, Jumagaziyeva AB, Suldina NA, Ilin AI. The Effect of Iodine-Containing Nano-Micelles, FS-1, on Antibiotic Resistance, Gene Expression and Epigenetic Modifications in the Genome of Multidrug Resistant MRSA Strain Staphylococcus aureus ATCC BAA-39. Front Microbiol 2020; 11:581660. [PMID: 33193215 PMCID: PMC7642360 DOI: 10.3389/fmicb.2020.581660] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 09/18/2020] [Indexed: 12/14/2022] Open
Abstract
Application of supplementary drugs which increase susceptibility of pathogenic bacteria to antibiotics is a promising yet unexplored approach to overcome the global problem of multidrug-resistant infections. The discovery of a new drug, an iodine-containing nano-molecular complex FS-1, which has proven to improve susceptibility to antibiotics in various pathogens, including MRSA strain Staphylococcus aureus ATCC BAA-39TM, allowed studying this phenomenon. Chromosomal DNA and total RNA samples extracted from the FS-1 treated strain (FS) and from the negative control (NC) cultures were sequenced by PacBio SMRT and Ion Torrent technologies, respectively. PacBio DNA reads were used to assemble chromosomal DNA of the NC and FS variants of S. aureus BAA-39 and to perform profiling of epigenetically modified nucleotides. Results of transcriptional profiling, variant calling and detection of epigenetic modifications in the FS variant were compared to the NC variant. Additionally, the genetic alterations caused by the treatment of S. aureus BAA-39 with FS-1 were compared to the results of a similar experiment conducted with another model organism, E. coli ATCC BAA-196. Several commonalities in responses of these phylogenetically distant microorganisms to the treatment with FS-1 were discovered, which included metabolic transition toward anaerobiosis and oxidative/osmotic stress response. S. aureus culture appeared to be more sensitive to FS-1 due to a higher penetrability of cells by iodine bound compounds, which caused carbonyl stress associated with nucleotide damaging by FS-1, abnormal epigenetic modifications and an increased rate of mutations. It was hypothesized that the disrupted pattern of adenine methylated loci within methicillin-resistance chromosome cassettes (SCCmec) may promote excision of this antibiotic resistance determinant from chromosomes while the altered pattern of cytosine methylation was behind the adaptive gene regulation in the culture FS. The selection against the antibiotic resistance in bacterial populations caused by abnormal epigenetic modifications exemplifies possible mechanisms of antibiotic resistance reversion induced by iodine-containing compounds. These finding will facilitate development of therapeutic agents against multidrug-resistant infections.
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Affiliation(s)
- Oleg N. Reva
- Centre for Bioinformatics and Computational Biology (CBCB), Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | | | - Monique Joubert
- Centre for Bioinformatics and Computational Biology (CBCB), Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Sergey V. Shilov
- Scientific Center for Anti-Infectious Drugs (SCAID), Almaty, Kazakhstan
| | | | | | - Alexandr I. Ilin
- Scientific Center for Anti-Infectious Drugs (SCAID), Almaty, Kazakhstan
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