Genomic analysis of two drug-resistant clinical Morganella morganii strains isolated from UTI patients in Pretoria, South Africa

Morganella morganii is an opportunistic bacterial pathogen of the Enterobacteriaceae family that is occasionally isolated from clinical (animal and human) specimens with varying resistance profiles. Detailed genomic analyses of drug‐resistant M. morganii strains are relatively limited, particularly in Africa, which is also due to their relatively low isolation rates from clinical settings. Here we report on two multidrug‐resistant clinical M. morganii isolates from urine specimens of two hospitalized patients in South Africa who presented with urinary tract infections in 2013. The isolates, M006 and E042, were only susceptible to carbapenems, amikacin and tigecycline. One strain, M006, had a novel class 1 integron, ln1484, associated with aadA7, sul1and gcuD gene cassettes and a Col3M plasmid replicase gene. The ln1484 intI1:aadA7:sul1 genes were bracketed by a TnAs3 composite transposon while a tet(B) gene was found on an IS4 family transposon. The rare blaDHA‐4 and blaDHA‐1 AmpC β‐lactamase genes were identified on the isolates’ chromosome. The isolates were phylogenetically distant and closely related to other international strains, suggesting that they were not obtained from a single epidemiological source. Further molecular surveillance is necessary to establish the prevalence of these MDR strains in the tertiary hospital. Moreover antibiotic stewardship and antibiotic sensitivity testing of all clinical isolates should be undertaken after empirical treatment to inform tailored therapy as well as reduce escalation of resistance and associated morbidities and mortalities.Supplementary Data S1. Metadata of isolates included in phylogenomic analysis.The National Health Laboratory Services (Grant No.: 94445), the University of Pretoria (Grant No.: A0702) and the South African Medical Research Council.https://onlinelibrary.wiley.com/journal/1472765x2021-01-01hj2020Medical Microbiolog

First report of a whole-genome shotgun sequence of a clinical Enterococcus faecalis sequence type 6 strain from South Africa

Enterococcus faecalis is a lactic acid-producing Gram-positive bacterium commonly found in the intestinal tract of humans and animals; it is implicated in multidrug-resistant nosocomial infections. The draft genome of this E. faecalis sequence type 6 (ST6) strain consists of 3,215,228 bp, with 37.20% GC content, 3,048 predicted coding sequences, and 61 RNA genes.Grant 94445 from the NHLShttp://genomea.asm.orgam2018Medical Microbiolog

Genomic analysis of a multidrug-resistant clinical Providencia rettgeri (PR002) strain with the novel integron ln1483 and an A/C plasmid replicon

Please read abstract in the article.Supplementary material: Figure S1. Prophages of P. rettgeri PR002 were identified using the PHAge Search Tool (PHAST). PR002 contained four intact prophages (red color), one incomplete prophage (gray color), and one questionable prophage (green color).Supplementary tables: Table S1. Metadata (biosample data) of all sequenced P. rettgeri isolates from NCBI GenBank database Table S2. Genes associated with general COG functional categories in the genome of P. rettgeri PR002. Table S3. Pathogenicity islands (PAIs) predicted for PR002 from VFDB (http://www.paidb.re.kr/about_paidb.php). Table S5. Diversity of metal resistance gene determinants found in PR002 genome.File S1. Metadata of isolates used in phylogenomics.The National Health Laboratory Services of South Africahttps://nyaspubs.onlinelibrary.wiley.com/journal/17496632hj2021Medical Microbiolog

Emergence of mcr-9.1 in extended-spectrum-β-lactamase-producing clinical Enterobacteriaceae in Pretoria, South Africa : global evolutionary phylogenomics, resistome, and mobilome

Extended-spectrum-β-lactamase (ESBL)-producing Enterobacteriaceae are critical-priority pathogens that cause substantial fatalities. With the emergence of mobile mcr genes mediating resistance to colistin in Enterobacteriaceae, clinicians are now left with few therapeutic options. Eleven clinical Enterobacteriaceae strains with resistance to cephems and/or colistin were genomically analyzed to determine their resistomes, mobilomes, and evolutionary relationships to global strains. The global phylogenomics of mcr genes and mcr-9.1-bearing genomes were further analyzed. Ten isolates were ESBL positive. The isolates were multidrug resistant and phylogenetically related to global clones but distant from local strains. Multiple resistance genes, including blaCTX-M-15 blaTEM-1, and mcr-9.1, were found in single isolates; ISEc9, IS19, and Tn3 transposons bracketed blaCTX-M-15 and blaTEM-1. Common plasmid types included IncF, IncH, and ColRNAI. mcr-9 was of close sequence identity to mcr-3, mcr-5, mcr-7, mcr-8, and mcr-10. Genomes bearing mcr-9.1 clustered into six main phyletic groups (A to F), with those of this study belonging to clade B. Enterobacter species and Salmonella species are the main hosts of mcr-9.1 globally, although diverse promiscuous plasmids disseminate mcr-9.1 across different bacterial species. Emergence of mcr-9.1 in ESBL-producing Enterobacteriaceae in South Africa is worrying, due to the restricted therapeutic options. Intensive One Health molecular surveillance might discover other mcr alleles and inform infection management and antibiotic choices. IMPORTANCE: Colistin is currently the last-resort antibiotic for difficult-to-treat bacterial infections. However, colistin resistance genes that can move from bacteria to bacteria have emerged, threatening the safe treatment of many bacterial infections. One of these genes, mcr-9.1, has emerged in South Africa in bacteria that are multidrug resistant, further limiting treatment options for clinicians. In this work, we show that this new gene is disseminating worldwide through Enterobacter and Salmonella species through multiple plasmids. This worrying observation requires urgent action to prevent further escalation of this gene in South Africa and Africa.Supplemental material: FIG S1. A dendrogram showing the phylogenetic relationship between mcr gene variants from different Gram-negative bacteria (chromosomes and plasmids). The bootstrap values are shown in red and represent the bootstrap values in Fig. 1B. TABLE S1. Antimicrobial sensitivity results and resistome of the isolates. The sensitivity of the isolates to the various antibiotics tested using MicroScan is shown, with those colored green being resistant according to the CLSI breakpoints. Those colored blue are resistant according to the EUCAST breakpoints. Those not colored are susceptible. The various antibiotic classes to which the antibiotic agents belong are shown above each antibiotic in unique colors, and the resistance genes per isolate are shown in the last column. DATA SET S1. General data of demographic, phenotypic, and genomic results used for this study. DATA SET S2. Sequences and alignment of contigs harboring the mcr-9.1 genes DATA SET S3. Sequences of mcr gene variants.http://msystems.asm.orgpm2020Medical Microbiolog

Pathogenomics and evolutionary epidemiology of multi-drug resistant clinical Klebsiella pneumoniae isolated from Pretoria, South Africa

Antibiotic-resistant Klebsiella pneumoniae is increasingly being implicated in invasive infections worldwide with high mortalities. Forty-two multidrug resistant (MDR) K. pneumoniae isolates were collected over a 4-month period. Antimicrobial susceptibility was determined using Microscan. The evolutionary epidemiology, resistome, virulome and mobilome of the isolates were characterised using whole-genome sequencing and bioinformatics analysis. All isolates contained the blaCTX-M gene, whilst 41/42(97%) contained blaTEM, 36/42(86%) contained blaOXA and 35/42(83%) harboured blaSHV genes. Other resistance genes found included blaLEN, aac(6′)-lb-cr, qnrA, qnrB, qnrS, oqxAB, aad, aph, dfr, sul1, sul2, fosA, and cat genes. Fluoroquinolone and colistin resistance-conferring mutations in parC, gyrAB, pmrAB, phoPQ and kpnEF were identified. The blaLEN gene, rarely described worldwide, was identified in four isolates. The isolates comprised diverse sequence types, the most common being ST152 in 7/42(17%) isolates; clone-specific O and K capsule types were identified. Diverse virulence genes that were not clone-specific were identified in all but one isolate. IncF, IncH and IncI plasmid replicons and two novel integrons were present. The blaCTX-M-15 and blaTEM-1 genes were bracketed by Tn3 transposons, ISEc9, a resolvase and IS91 insertion sequence. There were 20 gene cassettes in 14 different cassette arrays, with the dfrA and aadA gene cassettes being the most frequent. Phylogenetic analysis demonstrated that the isolates were evolutionarily associated with strains from both South Africa and abroad. These findings depict the rich resistome, mobilome and virulome repertoire in clinical K. pneumoniae strains, which are mainly transmitted by clonal, multiclonal and horizontal means in South Africa.Part of this work was presented at the International Society for Infectious Diseases (ISID) Congress, Buenos Aires, Argentina, 2018 (Abstract #1732) and the American Society of Microbiology (ASM) congress, Atlanta, USA 2018 (Abstract #5351).Supplementary information: Supplementary Table S1. Supplementary Table S2. Supplementary Data S3. Supplementary Data S4.The National Health Laboratories Services, the University of Pretoria and the South African Medical Research Council.http://www.nature.com/srepam2021Medical Microbiolog

The resistome, mobilome, virulome and phylogenomics of multidrug-resistant Escherichia coli clinical isolates from Pretoria, South Africa

Antibiotic-resistant Escherichia coli is a common occurrence in food, clinical, community and environmental settings worldwide. The resistome, mobilome, virulome and phylogenomics of 20 multidrug resistant (MDR) clinical E. coli isolates collected in 2013 from Pretoria, South Africa, were characterised. The isolates were all extended-spectrum β-lactamase producers, harbouring CTX-M (n = 16; 80%), TEM-1B (n = 10; 50%) and OXA (n = 12, 60%) β-lactamases alongside genes mediating resistance to fluoroquinolones, aminoglycosides, tetracyclines etc. Most resistance determinants were found on contigs containing IncF plasmid replicons and bracketed by composite transposons (Tn3), diverse ISs and class 1 integrons (In13, In54, In369, and In467). Gene cassettes such as blaOXA, dfrA5-psp-aadA2-cmlA1a-aadA1-qac and estX3-psp-aadA2-cmlA1a-aadA1a-qac were encompassed by Tn3 and ISs; several isolates had same or highly similar genomic antibiotic resistance islands. ST131 (n = 10), ST617 (n = 2) and singletons of ST10, ST73, ST95, ST410, ST648, ST665, ST744 and ST998 clones were phylogenetically related to clinical (human and animal) strains from Egypt, Kenya, Niger, Nigeria, Tanzania, and UK. A rich repertoire of virulence genes, including iss, gad and iha were identified. MDR E. coli harbouring chromosomal and plasmid-borne resistance genes in same and multiple clones exist in South Africa, which is very worrying for clinical epidemiology and infectious diseases management.The National Health Laboratory Services, the University of Pretoria and the South African Medical Research Council.http://www.nature.com/sreppm2020Medical Microbiolog

Draft genome sequence of a clinical Enterococcus faecium sequence type 18 strain from South Africa

We report the first draft genome sequence of an Enterococcus faecium sequence type 18 (ST18) strain isolated from a tuberculosis patient in Africa. The genome is comprised of 3,202,539 bp, 501 contigs, 37.70% GC content, 3,202 proteinencoding genes, and 61 RNA genes. The resistome and virulome of this important pathogen are presented herein.Grant 94445 of the National Health Laboratory Services of South Africa.http://genomea.asm.orgam2018Medical Microbiolog

First Report of a Whole-Genome Shotgun Sequence of a Clinical Enterococcus faecalis Sequence Type 6 Strain from South Africa

Enterococcus faecalis is a lactic acid-producing Gram-positive bacterium commonly found in the intestinal tract of humans and animals; it is implicated in multidrug-resistant nosocomial infections. The draft genome of this E. faecalis sequence type 6 (ST6) strain consists of 3,215,228 bp, with 37.20% GC content, 3,048 predicted coding sequences, and 61 RNA genes.Grant 94445 from the NHLShttp://genomea.asm.orgam2018Medical Microbiolog

Phylogenomic and epidemiological insights into two clinical Mycobacterium bovis BCG strains circulating in South Africa

BACKGROUND : Mycobacterium bovis BCG is a live, attenuated tuberculosis vaccine. While the vaccine protects infants from tuberculosis, complications including disseminated infections have been reported following vaccination. Genetically diverse BCG sub-strains now exist following continuous passaging of the original Pasteur strain for vaccine manufacture. This genetic diversity reportedly influences the severity of disseminated BCG infections and the efficacy of BCG immunization. METHODS : M. bovis BCG was isolated from infants suspected of being infected with tuberculosis. The whole genome of the clinical isolates and BCG Moscow were sequenced using Illumina Miseq and the sequences were analysed using CLC Genomics Workbench 7.0, PhyResSE v1.0, and Parsnp. RESULTS AND CONCLUSIONS : Genetic variations between the clinical strains and the reference BCG Copenhagen were identified. The clinical strains shared only one mutation in a secretion protein. Mutations were identified in various antibiotic resistance genes in the BCG isolates, which suggests their potential as multidrug-resistant (MDR) phenotypes. Phylogenetic analysis showed that the two isolates were distantly related, and the M1_S48 clinical isolate was closely related to M. bovis BCG Moscow. The phylogenomics results imply that two different BCG strains may be circulating in South Africa. However, it is difficult to associate the BCG vaccine strain administered and the BCG strain supplied with specific adverse events, as BCGiosis is under-reported. This study presents background genomic information for future surveillance and tracking of the distribution of BCGiosis-associated mycobacteria. It is also the first to report on the genomes of clinical BCG strains in Africa.Supplementary material: Table S1We would like to acknowledge the Department of Microbiol- ogy, National Health Laboratory Services/Tshwane Academic Division for providing the BCG isolates and funding the study, the Department of Medical Microbiology, University of Pretoria for providing facilities to conduct the study, and the National Institute of Communicable Diseases for sequencing the BCG isolates. We would also like to offer our gratitude to Mrs O.O. Onwegbuna for her assistance with sample collection and her laboratory expertise.The Department of Microbiology, National Health Laboratory Services/Tshwane Academic Division.http://www.elsevier.com/locate/ijidam2020BiochemistryGeneticsMedical MicrobiologyMicrobiology and Plant Patholog