Papers by Mustapha Mustapha
SummaryBackgroundHealthcare-associated bacterial pathogens frequently carry plasmids that contrib... more SummaryBackgroundHealthcare-associated bacterial pathogens frequently carry plasmids that contribute to antibiotic resistance and virulence. The horizontal transfer of plasmids in healthcare settings has been previously documented, but genomic and epidemiologic methods to study this phenomenon remain underdeveloped. The objectives of this study were to develop a method to systematically resolve and track plasmids circulating in a single hospital, and to identify epidemiologic links that indicated likely horizontal plasmid transfer.MethodsWe derived empirical thresholds of plasmid sequence similarity from comparisons of plasmids carried by bacterial isolates infecting individual patients over time, or involved in hospital outbreaks. We then applied those metrics to perform a systematic screen of 3,074 genomes of nosocomial bacterial isolates from a single hospital for the presence of 89 plasmids. We also collected and reviewed data from electronic health records for evidence of geote...
PLOS Pathogens, 2021
Meningococcal disease is a life-threatening illness caused by the human-restricted bacterium Neis... more Meningococcal disease is a life-threatening illness caused by the human-restricted bacterium Neisseria meningitidis. Outbreaks in the USA involve at least two cases in an organization or community caused by the same serogroup within three months. Genome comparisons, including phylogenetic analysis and quantification of genome distances can provide confirmatory evidence of pathogen transmission during an outbreak. Interpreting genome distances depends on understanding their distribution both among isolates from outbreaks and among those not from outbreaks. Here, we identify outbreak strains based on phylogenetic relationships among 141 N. meningitidis isolates collected from 28 outbreaks in the USA during 2010–2017 and 1516 non-outbreak isolates collected through contemporaneous meningococcal surveillance. We show that genome distance thresholds based on the maximum SNPs and allele distances among isolates in the phylogenetically defined outbreak strains are sufficient to separate mo...
The Journal of Infectious Diseases, 2020
Background The mechanisms by which Neisseria meningitidis cause persistent human carriage and tra... more Background The mechanisms by which Neisseria meningitidis cause persistent human carriage and transition from carriage to invasive disease have not been fully elucidated. Methods Georgia and Maryland high school students were sampled for pharyngeal carriage of N. meningitidis during the 2006–2007 school year. A total of 321 isolates from 188 carriers and all 67 invasive disease isolates collected during the same time and from the same geographic region underwent whole-genome sequencing. Core-genome multilocus sequence typing was used to compare allelic profiles, and direct read mapping was used to study strain evolution. Results Among 188 N. meningitidis culture–positive students, 98 (52.1%) were N. meningitidis culture positive at 2 or 3 samplings. Most students who were positive at >1 sampling (98%) had persistence of a single strain. More than a third of students carried isolates that were highly genetically related to isolates from other students in the same school, and occas...
Clinical Infectious Diseases, 2020
Background Traditional methods of outbreak investigations utilize reactive whole genome sequencin... more Background Traditional methods of outbreak investigations utilize reactive whole genome sequencing (WGS) to confirm or refute the outbreak. We have implemented WGS surveillance and a machine learning (ML) algorithm for the electronic health record (EHR) to retrospectively detect previously unidentified outbreaks and to determine the responsible transmission routes. Methods We performed WGS surveillance to identify and characterize clusters of genetically-related Pseudomonas aeruginosa infections during a 24-month period. ML of the EHR was used to identify potential transmission routes. A manual review of the EHR was performed by an infection preventionist to determine the most likely route and results were compared to the ML algorithm. Results We identified a cluster of 6 genetically related P. aeruginosa cases that occurred during a 7-month period. The ML algorithm identified gastroscopy as a potential transmission route for 4 of the 6 patients. Manual EHR review confirmed gastrosc...
eLife, 2020
Multidrug-resistant bacteria pose a serious health threat, especially in hospitals. Horizontal ge... more Multidrug-resistant bacteria pose a serious health threat, especially in hospitals. Horizontal gene transfer (HGT) of mobile genetic elements (MGEs) facilitates the spread of antibiotic resistance, virulence, and environmental persistence genes between nosocomial pathogens. We screened the genomes of 2173 bacterial isolates from healthcare-associated infections from a single hospital over 18 months, and identified identical nucleotide regions in bacteria belonging to distinct genera. To further resolve these shared sequences, we performed long-read sequencing on a subset of isolates and generated highly contiguous genomes. We then tracked the appearance of ten different plasmids in all 2173 genomes, and found evidence of plasmid transfer independent from bacterial transmission. Finally, we identified two instances of likely plasmid transfer within individual patients, including one plasmid that likely transferred to a second patient. This work expands our understanding of HGT in hea...
Emerging Infectious Diseases, 2020
We describe 2 human cases of infection with a new Neisseria species (putatively N. brasiliensis),... more We describe 2 human cases of infection with a new Neisseria species (putatively N. brasiliensis), 1 of which involved bacteremia. Genomic analyses found that both isolates were distinct strains of the same species, were closely related to N. iguanae, and contained a capsule synthesis operon similar to N. meningitidis.
Multidrug-resistant bacterial pathogens pose a serious public health threat, especially in hospit... more Multidrug-resistant bacterial pathogens pose a serious public health threat, especially in hospital settings. Horizontal gene transfer (HGT) of mobile genetic elements (MGEs) contributes to this threat by facilitating the rapid spread of genes conferring antibiotic resistance, enhanced virulence, and environmental persistence between nosocomial pathogens. Despite recent advances in microbial genomics, studies of HGT in hospital settings remain limited in scope. The objective of this study was to identify and track the movement of MGEs within a single hospital system using unbiased methods. We screened the genomes of 2,173 bacterial isolates from healthcare-associated infections collected over an 18-month time period to identify nucleotide regions that were identical in the genomes of bacteria belonging to distinct genera. These putative MGEs were found in 196 isolates belonging to 11 different genera; they grouped into 51 clusters of related elements, and they were most often shared...
Open Forum Infectious Diseases, 2019
Background CRAb is a major cause of healthcare-associated infections and is associated with high ... more Background CRAb is a major cause of healthcare-associated infections and is associated with high mortality due to the lack of reliable treatment options. We aimed to elucidate the contemporary population structure of CRAb isolates circulating in US hospitals using whole-genome sequencing (WGS). Methods A total of 131 CRAb isolates were identified at four tertiary care medical centers located in Ohio, Pennsylvania, Texas and North Carolina between 2017 and 2018. The genomes were sequenced with Illumina NextSeq and de novo assembled. Sequence types (STs) were identified using the Pasteur Institute MLST scheme. β-Lactamase genes were identified by ResFinder and manually curated. Results The 131 isolates belonged to 10 different ST types, including 8 known and 2 novel ones. In this collection, 101 isolates (77.1%) belonged to ST2, the dominant drug-resistant clone in the United States and Europe; 20 isolates belonged to ST499, a less common, but also globally distributed clone. Two isol...
Antimicrobial Agents and Chemotherapy, 2019
OXA-232 is an OXA-48-group class D β-lactamase that hydrolyzes expanded-spectrum cephalosporins a... more OXA-232 is an OXA-48-group class D β-lactamase that hydrolyzes expanded-spectrum cephalosporins and carbapenems at low levels. Clinical strains producing OXA-232 are sometimes susceptible to carbapenems, making it difficult to identify them in the clinical microbiology laboratory.
mBio, 2019
The carbapenem class of antibiotics is invaluable for the treatment of selected multidrug-resista... more The carbapenem class of antibiotics is invaluable for the treatment of selected multidrug-resistant Gram-negative pathogens. The continued transmission of carbapenem-resistant bacteria such as ST258 K. pneumoniae is of serious global public health concern, as treatment options for these infections are limited. This genomic epidemiologic investigation traced the natural history of ST258 K. pneumoniae in a single health care setting over nearly a decade. We found that distinct ST258 subpopulations have caused both device-associated and ward-associated outbreaks, and some of these populations remain endemic within our hospital to the present day. The finding of virulence determinants among emergent ST258 clones supports the idea of convergent evolution of drug-resistant and virulent CRKP strains and highlights the need for continued surveillance, prevention, and control efforts to address emergent and evolving ST258 populations in the health care setting.
Antimicrobial Agents and Chemotherapy, 2019
We report patient-to-patient transmission of Enterobacter hormaechei isolates with reduced suscep... more We report patient-to-patient transmission of Enterobacter hormaechei isolates with reduced susceptibility to ceftazidime-avibactam due to production of KPC-40, a variant of KPC-3 with a two-amino-acid insertion in the Ω-loop region (L167_E168dup). The index patient had received a prolonged course of ceftazidime-avibactam therapy, whereas the second patient had not received the agent and still became colonized with the KPC-40-producing strain.
Infection Control & Hospital Epidemiology, 2019
Background:Identifying routes of transmission among hospitalized patients during a healthcare-ass... more Background:Identifying routes of transmission among hospitalized patients during a healthcare-associated outbreak can be tedious, particularly among patients with complex hospital stays and multiple exposures. Data mining of the electronic health record (EHR) has the potential to rapidly identify common exposures among patients suspected of being part of an outbreak.Methods:We retrospectively analyzed 9 hospital outbreaks that occurred during 2011–2016 and that had previously been characterized both according to transmission route and by molecular characterization of the bacterial isolates. We determined (1) the ability of data mining of the EHR to identify the correct route of transmission, (2) how early the correct route was identified during the timeline of the outbreak, and (3) how many cases in the outbreaks could have been prevented had the system been running in real time.Results:Correct routes were identified for all outbreaks at the second patient, except for one outbreak i...
Journal of Antimicrobial Chemotherapy, 2018
Open Forum Infectious Diseases, 2018
June 2017 to December 2017. The automated PCR test was performed directly from respiratory specim... more June 2017 to December 2017. The automated PCR test was performed directly from respiratory specimens. The results were compared with in-house PCR for detection of carbapenemase genes performed on KP colonies isolated from respiratory specimens as our reference method. Patient and clinical characteristics between patients with CPK and non-CPK were also analyzed. Results. The prevalence of CPK was 10.6% (18/169 isolates). The automated PCR test had 91.12% accuracy, 66.7% sensitivity (95% CI, 40.9-86.6), 94.0% specificity (95% CI, 88.9-86.6), 57.1% positive predictive value (95% CI, 39.5-73.1) and 95.9% negative predictive value (95% CI, 92.48-97.85). Of 18 isolates, bla OXA-48 was the most common carbapenemase gene (17 isolates; 94.4%), followed by bla NDM-1 (7 isolates; 38.9%). A combination of bla OXA-48 and bla NDM-1 was detected in 6 isolates (33.3%). There were 7 (38.8%) colonizations and 11 (61.1%) infections. The significant risk factors for CPK included post-surgery (P = 0.04) and prior antibiotics exposure (P = 0.04). There was a trend toward higher mortality in patients with CPK albeit not significantly (33% vs. 24.5%, P = 0.41). Conclusion. The automated PCR test has an acceptable accuracy with fair sensitivity for the detection of carbapenemase genes. It is unique that OXA-48 and OXA-48/ NDM-1 are the most common carbapenemases in our institute. This diagnostic test may be use for rapid diagnosis or infection control purposes. Exposure to antibiotics associated with colonization or infection with CPK. Patients with CPK had higher mortality. Disclosures. All authors: No reported disclosures.
Infectious diseases (London, England), Sep 6, 2018
The aim of this study is to describe the molecular epidemiology of Neisseria meningitidis invasiv... more The aim of this study is to describe the molecular epidemiology of Neisseria meningitidis invasive disease before the introduction of serogroup C conjugate vaccine in Amazonas State in 2010. Meningococcal disease reported cases were investigated in Amazonas State during the period 2000-2010. N. meningitidis isolates (n = 196) recovered from patients were genotyped by multilocus sequence typing (MLST) and sequencing of porB, porA, fetA, fHbp and penA. Antimicrobial susceptibility was determined using E-test. In the study period, 948 cases were reported; the incidence was 2.8 for the entire state and 4.8 per 100,000 in the capital of Manaus. Most meningococcal disease was caused by N. meningitidis belonging to ST-32 (72%; 141/196) or ST-103 (21%; 41/196) clonal complexes. Capsular switching (B→C) was suggested within clonal complex (cc) 32. There were 6 (3%; 6/196) strains with intermediate susceptibility to penicillin and a single strain was resistant to rifampicin. Since 2007, serog...
Emerging infectious diseases, 2018
The expansion of hypervirulent sequence type 4821 clonal complex (CC4821) lineage Neisseria menin... more The expansion of hypervirulent sequence type 4821 clonal complex (CC4821) lineage Neisseria meningitidis bacteria has led to a shift in meningococcal disease epidemiology in China, from serogroup A (MenA) to MenC. Knowledge of the evolution and genetic origin of the emergent MenC strains is limited. In this study, we subjected 76 CC4821 isolates collected across China during 1972-1977 and 2005-2013 to phylogenetic analysis, traditional genotyping, or both. We show that successive recombination events within genes encoding surface antigens and acquisition of quinolone resistance mutations possibly played a role in the emergence of CC4821 as an epidemic clone in China. MenC and MenB CC4821 strains have spread across China and have been detected in several countries in different continents. Capsular switches involving serogroups B and C occurred among epidemic strains, raising concerns regarding possible increases in MenB disease, given that vaccines in use in China do not protect agai...
Journal of clinical microbiology, 2017
Fosfomycin maintains activity against most Escherichia coli clinical isolates, but growth of E. c... more Fosfomycin maintains activity against most Escherichia coli clinical isolates, but growth of E. coli colonies within the zone of inhibition around the fosfomycin disk is occasionally observed upon susceptibility testing. We aimed to estimate the frequency of such non-susceptible inner colony mutants and identify the underlying resistance mechanisms. Disk diffusion testing of fosfomycin was performed on 649 multidrug-resistant E. coli clinical isolates collected between 2011 and 2015. For those producing inner colonies inside the susceptible range, the parental strains and their representative inner colony mutants were subjected to MIC testing, whole genome sequencing, qRT-PCR, and carbohydrate utilization studies. Of the 649 E. coli clinical isolates, 5 (0.8%) consistently produced non-susceptible inner colonies. Whole genome sequencing revealed deletion of uhpT encoding hexose-6-phosphate antiporter in 4 of the E. coli inner colony mutants, while the remaining mutant contained a no...
mBio, 2017
Fosfomycin is a decades-old antibiotic which is being revisited because of its perceived activity... more Fosfomycin is a decades-old antibiotic which is being revisited because of its perceived activity against many extensively drug-resistant Gram-negative pathogens. FosA proteins are Mn 2+ and K + -dependent glutathione S -transferases which confer fosfomycin resistance in Gram-negative bacteria by conjugation of glutathione to the antibiotic. Plasmid-borne fosA variants have been reported in fosfomycin-resistant Escherichia coli strains. However, the prevalence and distribution of fosA in other Gram-negative bacteria are not known. We systematically surveyed the presence of fosA in Gram-negative bacteria in over 18,000 published genomes from 18 Gram-negative species and investigated their contribution to fosfomycin resistance. We show that FosA homologues are present in the majority of genomes in some species (e.g., Klebsiella spp., Enterobacter spp., Serratia marcescens , and Pseudomonas aeruginosa ), whereas they are largely absent in others (e.g., E. coli , Acinetobacter baumannii...
Genome Announcements, 2016
We present here the draft genome sequences of four Pseudomonas putida isolates belonging to a sin... more We present here the draft genome sequences of four Pseudomonas putida isolates belonging to a single clone suspected for nosocomial transmission between patients and a bronchoscope in a tertiary hospital. The four genome sequences belong to a single lineage but contain differences in their mobile genetic elements.
Genome biology and evolution, Jul 11, 2016
Neisseria meningitidis is an important cause of meningococcal disease globally. Sequence type (ST... more Neisseria meningitidis is an important cause of meningococcal disease globally. Sequence type (ST)-11 clonal complex (cc11) is a hypervirulent meningococcal lineage historically associated with serogroup C capsule and is believed to have acquired the W capsule through a C to W capsular switching event. We studied the sequence of capsule gene cluster (cps) and adjoining genomic regions of 524 invasive W cc11 strains isolated globally. We identified recombination breakpoints corresponding to two distinct recombination events within W cc11: a 8.4 kb recombinant region likely acquired from W cc22 including the sialic acid/ glycosyl-transferase gene, csw resulted in a C→W change in capsular phenotype and a 13.7 kb recombinant segment likely acquired from Y cc23 lineage includes 4.5 kb of cps genes and 8.2 kb downstream of the cps cluster resulting in allelic changes in capsule translocation genes. A vast majority of W cc11 strains (497/524, 94.8%) retain both recombination events as evid...
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Papers by Mustapha Mustapha