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

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

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

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

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

Antimicrobial resistance patterns of Acinetobacter baumannii and Klebsiella pneumoniae isolated from dogs presented at a veterinary academic hospital in South Africa

Background and Aim: Acinetobacter baumannii and Klebsiella pneumoniae are opportunistic bacterial pathogens responsible for hospital-acquired infections in veterinary medicine. Infection with these bacteria always requires urgent antimicrobial therapy. However, there is no evidence of studies that have investigated the antimicrobial drug resistance profile of these organisms in a veterinary setting in South Africa. This study investigated the antimicrobial resistance (AMR) patterns of A. baumannii and K. pneumoniae from clinical specimens obtained from dogs presented at a veterinary academic hospital. The findings of this study contribute to an improved understanding of the AMR profile of these bacteria in veterinary medicine. Materials and Methods: Retrospective data of clinical samples from dogs that were positive for A. baumannii and K. pneumoniae between 2007 and 2013 were used in this study. The antimicrobial susceptibility of the isolates was determined using the disk diffusion method following the Clinical and Laboratory Standards Institute guidelines. The A. baumannii isolates were subjected to a panel of 20 antibiotics, while K. pneumoniae isolates were subjected to a panel of 22 antibiotics. Data were analyzed using descriptive statistics and presented using tables and figures. Results: Twenty (n = 20) A. baumannii isolates were isolated from bronchoalveolar lavage, foreign objects, bone, urine, skin, blood, ear, nasal, and oral cavity. Almost all A. baumannii (95%, 19/20) isolates were resistant to at least one antibiotic, and 60% (12/20) were multidrug-resistant (MDR). Klebsiella pneumoniae (n = 56) was isolated from urine, foreign objects, abscesses, ears, eyes, tracheal aspirations, bronchoalveolar lavages, eyes, abdominal aspirates, anal glands, bones, and intestinal and lung biopsies. All K. pneumoniae (100%, 56/56) isolates were resistant to at least one antibiotic, and 98% (55/56) were MDR. Conclusion: Both A. baumannii and K. pneumoniae were isolated in various clinical tissue samples and exhibited a high prevalence of resistance to multiple antibiotics. In addition, these bacteria exhibited a high prevalence of resistance to β-lactam compared to other classes of antibiotics, which is likely to impact treatment options and patient prognosis