92 research outputs found
Antimicrobial Resistance in Staphylococci at the Human– Animal Interface
The widespread and often indiscriminate use of antimicrobials in animals is considered an important driving force behind the emergence and spread of antimicrobial-resistant bacteria. The emergence of livestock-associated methicillin-resistant Staphylococcus aureus and the description of a novel methicillin-resistant gene, mecC, have renewed concerns regarding the role of animals as reservoirs and a source for the evolution of novel, virulent zoonotic pathogens. The transfer of antimicrobial-resistant bacteria residing in, or on, animals to close human contacts or the introduction of the bacteria into the food supply chain is a cause for concern. The purpose of this mini-review is to provide a background to the genus Staphylococcus and the emergence of antimicrobial resistance as well as a discussion on the most significant antimicrobial resistance mechanisms. The use of antimicrobials in animal husbandry is discussed and the interface between humans and different animal populations is closely examined. Finally, the need for antimicrobial monitoring programmes is discussed and is supplemented with information pertaining to antimicrobial susceptibility testing and molecular typing of staphylococcal isolates
Review - Understanding β-lactamase Producing Klebsiella pneumoniae
Klebsiella pneumoniae is a nosocomial pathogen commonly implicated in hospital outbreaks with a propensity for antimicrobial resistance towards mainstay β-lactam antibiotics and multiple other antibiotic classes. The successful proliferation, transmission and infection of the Gram-negative bacterium can be attributed to a myriad of factors including host factors, environmental factors, virulence factors and a large repertoire of antibiotic resistance mechanisms. The poor treatment outcomes and limited treatment options are consequences of the successful pathogenesis and spread of antibiotic resistance in the increasingly common β-lactamase producing K. pneumoniae bacterium. The review briefly explores the biology, successful pathogenesis and antibiotic resistance of K. pneumoniae as well as the detection and characterisation techniques of important strains
Identification and characterization of Staphylococcus devriesei isolates from bovine intramammary infections in KwaZulu-Natal, South Africa
BACKGROUND : Coagulase-negative staphylococci (CoNS) are among the leading bacterial causes of bovine mastitis
in many dairy-producing countries. Among the challenges associated with the specific diagnosis of CoNS infections
is the biochemical heterogeneity of the species in the genus and the unavailability of accurate, cost-effective and
up-to-date diagnostic tests. A previous study investigating the diversity of CoNS associated with cases of bovine
mastitis in South Africa, resulted in six CoNS isolates which could not be identified despite the use of a
combination of different molecular assays. The identification and characterisation of the isolates was pursued
further in this study.
RESULTS : The six CoNS isolates in question were identified by sequencing multiple housekeeping genes (dnaJ,
hsp60, rpoB, 16S rRNA) and characterized through the use of matrix-assisted laser/desorption ionization time of
flight mass spectrometry (MALDI-TOF MS) and the Biolog GEN III Microplate™ bacterial identification system.
Sequencing of housekeeping genes identified the isolates as S. devriesei. This Staphylococcus species was only
described in 2010 and this is the first report documenting the isolation of S. devriesei from cases of bovine IMIs in
South Africa. Analysis of mass spectra generated by the six isolates showed intra-species variation which was also
observed when evaluating the metabolic profiles of the isolates using the Biolog GEN III system. Neither the MALDITOF
MS nor the Biolog database are currently populated with data relating to S. devriesei, resulting in the isolates
not being identified, in the case of MALDI-TOF MS analysis, or mis-identified as was observed with the Biolog GEN
III system.
CONCLUSIONS : The phenotyping data collected during this investigation provides useful information concerning
Staphylococcus devriesei which could be used to populate user system databases thereby ensuring the accurate
identification of isolates in future. The availability of improved diagnostics will in turn facilitate studies to elucidate
the epidemiology, pathogenicity and true prevalence of this species in dairy herds.The research presented herein is funded, in part, by the University of
Pretoria, National Health Laboratory Services, RESCOM, the National Research
Foundation (NRF) Research Technology Fund and the KZN Department of
Agriculture and Rural Development. The MALDI-TOF MS work is supported in
part by the National Research Foundation (NRF) of South Africa (Grant
specific unique reference number, UID 74426).https://bmcvetres.biomedcentral.comMedical Microbiolog
Diversity and antimicrobial susceptibility profiling of staphylococci isolated from bovine mastitis cases and close human contacts
The objectives of this study were to examine the
diversity of Staphylococcus spp. recovered from bovine
intramammary infections and humans working in close
contact with the animals and to evaluate the susceptibility
of the staphylococcal isolates to different antimicrobials.
A total of 3,387 milk samples and 79 human
nasal swabs were collected from 13 sampling sites in
the KwaZulu-Natal province of South Africa. In total,
146 Staph. aureus isolates and 102 coagulase-negative
staphylococci (CNS) were recovered from clinical and
subclinical milk samples. Staphylococcus aureus was
isolated from 12 (15.2%) of the human nasal swabs and
95 representative CNS were recovered for further characterization.
The CNS were identified using multiplex-
PCR assays, matrix-assisted laser desorption/ionization
time-of-flight mass spectrometry (MALDI-TOF
MS), and tuf gene sequencing. Seven Staphylococcus
spp. were identified among the CNS of bovine origin,
with Staph. chromogenes (78.4%) predominating. The
predominant CNS species recovered from the human
nasal swabs was Staph. epidermidis (80%) followed by
Staph. chromogenes (6.3%). The antimicrobial susceptibility
of all staphylococcal isolates was evaluated using
disk diffusion and was supplemented by screening for
specific antimicrobial resistance genes. Ninety-eight
(67.1%) Staph. aureus isolates of bovine origin were
pansusceptible; 39 (26.7%) isolates were resistant to
a single class, and 7 (4.8%) isolates were resistant to
2 classes of antimicrobials. Two Staph. aureus (1.4%)
isolates were multidrug-resistant. Resistance to penicillin
was common, with 28.8% of the bovine and 75% of
the human Staph. aureus isolates exhibiting resistance.
A similar observation was made with the CNS, where
37.3% of the bovine and 89.5% of the human isolates
were resistant to penicillin. Multidrug-resistance was
common among the human CNS, with 39% of the
isolates exhibiting resistance to 3 or more classes of antimicrobials. The antimicrobial susceptibility results
suggest that resistance among staphylococci causing
bovine intramammary infections in South Africa is uncommon
and not a significant cause for concern. In contrast,
antimicrobial resistance was frequently observed
in staphylococcal isolates of human origin, highlighting
a possible reservoir of resistance genes. Continued
monitoring of staphylococcal isolates is warranted to
monitor changes in the susceptibility of isolates to different
classes of antimicrobials.University of Pretoria, RESCOM, the National Research Foundation (NRF) of
South Africa, and the KZN Department of Agriculture & Rural Development (South Africa).http://www.journals.elsevier.com/journal-of-dairy-science2016-09-30hb201
Prevalence of Clostridium difficile toxin genes in Pretoria
The hypervirulent polymerase chain reaction (PCR) ribotype 027 strain of Clostridium difficile produces toxins A, B and a binary
toxin. Toxin detection kits are commonly used in diagnostic laboratories, but have been unsuccessful in detecting all of the
relevant C. difficile strains, and the toxins produced. In this study, conventional PCR was used to detect the presence of the genes
of toxin A, toxin B and the binary toxin of C. difficile. Eighty-four frozen (collected between 2006-2007) and 13 fresh (collected in
2010) stool specimens, obtained in Pretoria, were analysed. The genes for toxin A, toxin B and the binary toxin were detected in
one of the fresh stool specimens. This may have implications for healthcare facilities, and suggests the possible emergence of
the highly virulent PCR ribotype 027 strain of C. difficile in Pretoria. This emphasises the importance of continuous surveillance
and monitoring of C. difficile outbreaks.http://www.sajei.co.za/index.php/SAJEIay201
Detection of the Janus kinase 2 V617F mutation using a locked nucleic-acid, real-time polymerase chain reaction assay
The purpose of this study was to develop a real time polymerase chain reaction (PCR) assay
for the detection of the JAK2 V617F mutation that could be used in diagnostic laboratories.
Sanger sequencing and a newly developed locked nucleic-acid, real-time PCR assay were used
to detect the JAK2 V617F mutation. There was 100% agreement between the sequencing and
PCR analysis. Both assays were able to detect the mutation in all 24 of the 60 test specimens
harbouring the mutation.The National Health Laboratory
Service research trusthttp://www.ajlmonline.orgam2019Haematolog
High prevalence of oxacillinases in clinical multidrug-resistant Acinetobacterbaumannii isolates from the Tshwane region, South Africa - an update
BACKGROUND : Acinetobacter baumannii is an important hospital-acquired pathogen in healthcare facilities that
frequently causes bacteraemia and ventilator-associated pneumonia in intensive care units. Acinetobacter baumannii
can be isolated from various sites in the hospital environment like medical equipment, bed linen, medical personnel
and indwelling catheters. It is difficult to treat A. baumannii infections because of their highly resistant antimicrobial
profiles. The purpose of this study was to determine the prevalence of β-lactamase genes in multidrug-resistant (MDR)
clinical A. baumannii isolates using Multiplex-PCR (M-PCR) assays.
METHODS : One hundred MDR A. baumannii isolates were collected from the diagnostic division of the Department of
Medical Microbiology after routine analysis of the submitted specimens. All collected isolates were identified and tested
for susceptibility using the VITEK 2® system (bioMérieux, France). Six isolates were excluded from this study because the
isolates were incorrectly identified as A. baumannii with the VITEK 2® system (bioMérieux, France). Molecular tests, namely
M-PCR assays, pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) were performed. MLST
analyses were performed on representative isolates from the four major pulsotypes (≥5 isolates with 80 % similarity) and
selective isolates from each minor pulsotype.
RESULTS : All the A. baumannii isolates showed 100 % resistance to ampicillin, amoxicillin, cefuroxime, cefuroximine axetil,
cefoxitin, cefotaxime and nitrofurantoin. Seven percent of the isolates were resistant to amikacin. Two percent of the
isolates were classified as having intermediate susceptibility to tigecycline. A. baumannii isolates showed an antibiotic
resistance profile of 67 % and higher to antibiotics, such as ceftazidime, cefepime, imipenem, meropenem, gentamicin,
ciprofloxacin and trimethoprim/sulfamethoxazole. None of the isolates were resistant to colistin. The M-PCR assays
showed that 99 % of the isolates contained the OXA-51 gene and 77 % contained the OXA-23 gene. None of the
isolates contained the GES, GIM, IMP, KPC, NDM, OXA-24, OXA-58, PER, SIM, SPM, VEB and VIM genes. Representative A.
baumannii isolates were grouped into five existing sequence types (ST): ST106, ST258, ST339, ST502, ST758 and ST848.
Isolates belonging to the pan-European clonal lineages I and II (EUI and EUII) were identified.
CONCLUSION : The high prevalence of MDR A. baumannii isolates has a severe impact on available treatment choices and
this in return impacts on treatment outcomes in the studied healthcare facilities. The most dominant ST among the
collected isolates was ST758, member of the EUI group. The presence of the OXA-23 gene was not restricted to a
specific ST. Continuous research and surveillance is necessary to monitor the circulating β-lactamase genes in clinical
settings to guide infection control policies in order to try and curb the spread of this bacterium.ML was supported by a
National Research Foundation (NRF) grant. The MALDI-TOF analysis is based on
research supported in part by the National Research Foundation (NRF) of South
Africa (Grant specific unique reference number (UID) 74426).http://www.biomedcentral.com/bmcinfectdis/am201
Bacterial vaginosis : current diagnostic avenues and future opportunities
A healthy female genital tract harbors a microbiome dominated by lactic acid and
hydrogen peroxide producing bacteria, which provide protection against infections by
maintaining a low pH. Changes in the bacterial compositions of the vaginal microbiome
can lead to bacterial vaginosis (BV), which is often associated with vaginal inflammation.
Bacterial vaginosis increases the risk of acquiring sexually transmitted infections (STIs)
like human immunodeficiency virus (HIV) and affects women’s reproductive health
negatively. In pregnant women, BV can lead to chorioamnionitis and adverse pregnancy
outcomes, including preterm premature rupture of the membranes and preterm birth. In
order to manage BV effectively, good diagnostic procedures are required. Traditionally
clinical and microscopic methods have been used to diagnose BV; however, these
methods require skilled staff and time and suffer from reduced sensitivity and specificity.
New diagnostics, including highly sensitive and specific point-of-care (POC) tests,
treatment modalities and vaccines can be developed based on the identification of
biomarkers from the growing pool of vaginal microbiome and vaginal metabolome data.
In this review the current and future diagnostic avenues will be discussed.http://www.frontiersin.org/Cellular_and_Infection_Microbiologyam2020BiochemistryGeneticsMedical MicrobiologyMicrobiology and Plant Patholog
Hospital-acquired and zoonotic bacteria from a veterinary hospital and their associated antimicrobial-susceptibility profile : a systematic review
DATA AVAILABILITY STATEMENT : The original contributions presented in the study are
included in the article/Supplementary material, further inquiries
can be directed to the corresponding authors.BACKGROUND : Hospital-acquired infections (HAIs) are associated with increased
mortality, morbidity, and an economic burden due to costs associated with
extended hospital stays. Furthermore, most pathogens associated with HAIs
in veterinary medicine are zoonotic. This study used published data to
identify organisms associated with HAIs and zoonosis in veterinary medicine.
Furthermore, the study also investigated the antimicrobial-susceptibility profile
of these bacterial organisms.
METHODS : A systematic literature review was conducted in accordance with
the Preferred Reporting Items for Systematic Reviews and Meta-analyses
(PRISMA) guidelines. Search terms and five electronic databases were used
to identify studies published over 20 years (2000–2020). The risk of bias was
assessed using the “Strengthening the Reporting of Observational Studies in
Epidemiology-Vet” (STROBE-Vet) checklist.
RESULTS : Out of the identified 628 papers, 27 met the inclusion criteria for this
study. Most studies (63%, 17/27) included were either from small animal or
companion animal clinics/hospitals, while 5% (4/27) were from large animal
clinics/hospitals inclusive of bovine and equine hospitals. Hospital-acquired
bacteria were reported fromenvironmental surfaces (33%, 9/27), animal clinical
cases (29.6%, 8/27), and fomites such as cell phones, clippers, stethoscopes,
and computers (14.8%, 4/27). Staphylococcus spp. was the most (63%; 17/27)
reported organism, followed by Escherichia coli (19%; 5/27), Enterococcus
spp. (15%, 4/27), Salmonella spp. (15%; 4/27), Acinetobacter baumannii (15%,
4/27), Clostridioides di cile (4%, 1/27), and Pseudomonas aeruginosa (4%;
1/27). Multidrug-resistant (MDR) organisms were reported in 71% (12/17)
of studies linked to Methicillin-resistant Staphylococcus aureus (MRSA),
Methicillin-resistant Staphylococcus pseudintermedius (MRSP), Enterococcus
spp., Salmonella Typhimurium, A. baumannii, and E. coli. The mecA gene was identified in bothMRSA andMRSP, the blaCMY-2 gene in E. coli and Salmonella
spp., and the vanA gene in E. faecium isolate. Six studies reported organisms
from animals with similar clonal lineage to those reported in human isolates.
CONCLUSION : Organisms associated with hospital-acquired infections and
zoonosis have been reported from clinical cases, environmental surfaces, and
items used during patient treatment and care. Staphylococcus species is the
most reported organism in cases of HAIs and some isolates shared similar
clonal lineage to those reported in humans. Some organisms associated with
HAIs exhibit a high level of resistance and contain genes associated with
antibiotic resistance.https://www.frontiersin.org/journals/veterinary-science#am2024Medical MicrobiologyParaclinical SciencesSDG-03:Good heatlh and well-bein
Prevalence of carbapenem resistance genes in Acinetobacter baumannii isolated from clinical specimens obtained from an academic hospital in South Africa
Acinetobacter baumannii is an important cause of hospital-acquired infections. The occurrence of carbapenem resistance that is
caused by the carbapenem-hydrolysing class D β-lactamases and the metallo-β-lactamases (MBLs) limits the range of therapeutic
alternatives in treating A. baumannii infections. In this study, two multiplex polymerase chain reactions were performed to screen for both carbapenem-hydrolysing class D β-lactamases and MBL genes in 97 clinical isolates of A. baumannii. Oxacillinase (OXA)-51 had a prevalence of 83% (81/97), and OXA-23 had a prevalence of 59% (57/97). One isolate was positive for an MBL
[Verona integron-encoded metallo β-lactamases (VIM)]. Therefore, continuous surveillance and monitoring of A. baumannii is
crucial because of the high prevalence of antibiotic resistance genes.http://www.sajei.co.za/index.php/SAJEIam2013ay201
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