Detection and Molecular Characterization of Methicillin-Resistant Staphylococcus aureus from Table Eggs in Haripur, Pakistan

Genotypic diversity of staphylococcal enterotoxin B gene (seb) and its association with molecular characterization and antimicrobial resistance of Staphylococcus aureus from retail food

To investigate the expression pattern of staphylococcal enterotoxin B (SEB) in food and the genotypic diversity of SEB-encoding gene in association with molecular characteristics and antimicrobial resistance of S. aureus, 498 isolates from retail food were screened for seb gene and detected for SEB production in S. aureus. In addition, the seb nucleotide sequences, virulence genes, resistance genes, antimicrobial susceptibility and molecular characteristics of S. aureus were examined. A total of 45 (9.0 %) seb-positive S. aureus strains were identified, all of which expressed SEB. The detection rate of SEB-production strains was significantly higher from dairy-related sources than those from other sources (P < 0.05). In vitro simulations showed that S. aureus could grow and express SEB in both milk and pork, with SEB expression exceeding 20 ng/g after 1 day of storage at room temperature. There were 2 distinct SEB genotyping (SEB1 and SEB2) in the SEB amino acid sequences of the 45 isolates, including 4 amino acid differences (Ala-13Val, Ser14Ala, Asn192Ser, and Met222Leu). There was no significant difference (P > 0.05) in SEB production between SEB1 and SEB2 genotyping strains. Based on MLST clustering analysis, the same molecular type strains were found to have the same SEB genotyping, virulence gene profile, resistance gene profile and drug resistance profile. Among them, the dominant molecular types of SEB1 and SEB2 strains were CC1-ST188-t189 and CC59-ST59-t437, respectively. Compared to the CC1-ST188-t189 clonal strain, the CC59-ST59-t437 clonal strain carried a higher number of virulence and resistance genes and exhibited a broader resistance profile. Therefore, understanding the characteristics of the strains and their expression patterns in food can be effective in preventing food poisoning incidents.

Zoonotic sources and the spread of antimicrobial resistance from the perspective of low and middle-income countries

BACKGROUND

Antimicrobial resistance is an increasing challenge in low and middle-income countries as it is widespread in these countries and is linked to an increased mortality. Apart from human and environmental factors, animal-related drivers of antimicrobial resistance in low- and middle-income countries have special features that differ from high-income countries. The aim of this narrative review is to address the zoonotic sources and the spread of antimicrobial resistance from the perspective of low- and middle-income countries.

MAIN BODY

Contamination with extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli is highest in poultry (Africa: 8.9-60%, Asia: 53-93%) and there is a risk to import ESBL-producing E. coli through poultry meat in Africa. In aquacultures, the proportion of ESBL-producers among E. coli can be high (27%) but the overall low quality of published studies limit the general conclusion on the impact of aquacultures on human health. ESBL-producing E. coli colonization of wildlife is 1-9% in bats or 2.5-63% birds. Since most of them are migratory animals, they can disperse antimicrobial resistant bacteria over large distances. So-called 'filth flies' are a relevant vector not only of enteric pathogens but also of antimicrobial resistant bacteria in settings where sanitary systems are poor. In Africa, up to 72.5% of 'filth flies' are colonized with ESBL-producing E. coli, mostly conferred by CTX-M (24.4-100%). While methicillin-resistant Staphylococcus aureus plays a minor role in livestock in Africa, it is frequently found in South America in poultry (27%) or pork (37.5-56.5%) but less common in Asia (poultry: 3%, pork: 1-16%).

CONCLUSIONS

Interventions to contain the spread of AMR should be tailored to the needs of low- and middle-income countries. These comprise capacity building of diagnostic facilities, surveillance, infection prevention and control in small-scale farming.

Assessment of knowledge, perception, practices and drivers of antimicrobial resistance and antimicrobial usage among veterinarians in Pakistan

BACKGROUND

Antimicrobial resistance (AMR) and irrational antimicrobial usage (AMU) are a global problem, particularly evident in low- and middle-income countries including Pakistan. Our study aimed to assess the knowledge, attitudes and prescribing practices (KAP) of field veterinarians regarding AMR and AMU.

METHODS

A questionnaire-based online survey was conducted using Google forms to collect data on AMR and AMU from veterinary practitioners in Pakistan between July 25, 2020, and February 2, 2021. The questionnaire was comprised of four sections: 1) Demographic information of the respondents, 2) Knowledge about AMR, and AMU, 3) Antibiotic prescribing behavior, attitudes and influencing drivers and 4) Practices of respondents about AMU and drug disposal.

RESULTS

A total of 545 participants (Male 84%, Female 16%) completed the survey. The respondents' qualification (P = 0.008), gender (P = 0.007) and type of practitioner (P < 0.001) had a significant association with the mean knowledge score about AMR. Most of the veterinarians had never attended any training, symposium, or awareness session on AMR (63%) and methods to detect antibiotic residues (71%). Participating veterinarians frequently included "critically important antimicrobials" in their treatment regimens. Most veterinarians (60%) prescribed antibiotics for viral diseases. Our study showed that about 44% of veterinarians disposed of expired drugs in the garbage. Antibiotics were prescribed as mass medication and for prophylaxis by 59% and 33% of the veterinarians, respectively, while about 60% of the veterinarians prescribed antibiotics starting with double doses in their treatment regimens. Importantly, only 4% of the veterinarians recognized the concept of One Health. Male veterinarians had higher odds of prescribing mass medication (OR=3.07, P < 0.001) and use of antibiotics for disease prophylaxis (OR=2.31, P = 0.002) than females, whereas improper disposal of expired antimicrobials (OR=2.12, P = 0.003) was more common in female veterinarians. Government veterinarians had 2 (OR=1.95, P = 0.016) and 3 (OR=3.05, P < 0.001) times higher odds to prescribe antibiotics prophylactically and for mass treatments, respectively compared to full-time private veterinarians.

CONCLUSION

Our study identifies key factors influencing veterinarians' decision about antimicrobial prescription and highlights important shortcomings such as lack of training on rational use of antimicrobials, frequent use of antimicrobials for mass medication and prophylaxis, widespread use of critically important antimicrobials, and improper disposal practices. There is a dire need to improve knowledge of veterinary practitioners regarding AMR and to adopt a One Health approach to rationalize AMU at the national level in line with the regional and international guidelines.

Phenotypic and Genotypic Detection of Biofilm-Forming Staphylococcus aureus from Different Food Sources in Bangladesh

Staphylococcus aureus is a major foodborne pathogen. The ability of S. aureus to produce biofilm is a significant virulence factor, triggering its persistence in hostile environments. In this study, we screened a total of 420 different food samples and human hand swabs to detect S. aureus and to determine their biofilm formation ability. Samples analyzed were meat, milk, eggs, fish, fast foods, and hand swabs. S. aureus were detected by culturing, staining, biochemical, and PCR. Biofilm formation ability was determined by Congo Red Agar (CRA) plate and Crystal Violet Microtiter Plate (CVMP) tests. The icaA, icaB, icaC, icaD, and bap genes involved in the synthesis of biofilm-forming intracellular adhesion compounds were detected by PCR. About 23.81% (100/420; 95% CI: 14.17−29.98%) of the samples harbored S. aureus, as revealed by detection of the nuc gene. The CRA plate test revealed 20% of S. aureus isolates as strong biofilm producers and 69% and 11% as intermediate and non-biofilm producers, respectively. By the CVMP staining method, 20%, 77%, and 3% of the isolates were found to be strong, intermediate, and non-biofilm producers. Furthermore, 21% of S. aureus isolates carried at least one biofilm-forming gene, where icaA, icaB, icaC, icaD, and bap genes were detected in 15%, 20%, 7%, 20%, and 10% of the S. aureus isolates, respectively. Bivariate analysis showed highly significant correlations (p < 0.001) between any of the two adhesion genes of S. aureus isolates. To the best of our knowledge, this is the first study in Bangladesh describing the detection of biofilm-forming S. aureus from foods and hand swabs using molecular-based evidence. Our findings suggest that food samples should be deemed a potential reservoir of biofilm-forming S. aureus, which indicates a potential public health significance.

Epidemiology and molecular characterization of Staphylococcus aureus causing bovine mastitis in water buffaloes from the Hazara division of Khyber Pakhtunkhwa, Pakistan

Buffalo represent a major source of milk in Pakistan. However, production is impacted by the disease bovine mastitis. Mastitis causes significant economic losses, with Staphylococcus aureus (S. aureus) being one of its major causative agents. While much work has been done understanding the epidemiology of bovine mastitis in Pakistan, detailed molecular characterization of the associated S. aureus is unavailable. In the current study both the epidemiological and molecular characterization of S. aureus from bovine mastitis in the Hazara division of Pakistan are examined. S. aureus was isolated from 18.41% of the animals, and left quarters more prone to infection (69.6%) than right quarters (30.4%). Sub-clinical mastitis (75.31%) was more prevalent than clinical mastitis (24.69%), with infections evenly distributed amongst the eight districts. Molecular characterization revealed that only 19.6% of the isolates were methicillin-resistant, and four strains types identified, including ST9-t7867-MSSA, ST9-MSSA, ST101-t2078-MSSA, and ST22-t8934-MRSA-IVa. Antiseptic resistance genes were not detected in the isolates, and low levels of antibiotic resistance were also noted, however the methicillin-resistant strains had higher overall antibiotic resistance. This study represents the most complete molecular typing data for S. aureus causing bovine mastitis in the Hazara district of Pakistan, and the country as a whole.

Genetic Diversity of Staphylococcus aureus Strains from a Tertiary Care Hospital in Rawalpindi, Pakistan

Staphylococcus aureus is an important healthcare-associated bacterium that causes a multitude of infections in humans such as superficial skin and soft tissue infections, necrotizing pneumonia, foodborne illnesses and postsurgical infections. Treatment of S. aureus infections has become more complicated due to the emergence of Methicillin-Resistant Staphylococcus aureus (MRSA), some of which are multidrug resistant. The present study aimed to characterize S. aureus isolates from a tertiary care hospital in the Rawalpindi district of Pakistan. Staphylococci were isolated from 300 clinical samples collected from January 2018 to January 2019 and S. aureus isolates were tested for antimicrobial susceptibility and analyzed using Pulsed-Field Gel Electrophoresis (PFGE), Multi-Locus Sequence Typing (MLST), staphylococcal cassette chromosome mec (SCCmec) and spa typing. Approximately 25.3% (76/300) of the clinical samples were positive for S. aureus; of those, 88.2% (67/76) were mecA+ (MRSA). In addition to the β-lactam antibiotics, high levels of resistance were also found to the fluoroquinolones (ciprofloxacin, gatifloxacin and levofloxacin (73.7% each)). Of the 23 different spa types identified, the majority of isolates belonged to spa type t632 and t657 (9/66; 13.6% each spa type). ST772-t657 (Bengal Bay clone) was the most commonly identified clone in this study although other clones circulating around different regions of the world were also found indicating the diversity in MRSA isolates from this area of Pakistan. This study emphasizes the need to monitor MRSA in the clinical setting for improved infection control and treatment options.

Staphylococci in poultry intestines: a comparison between farmed and household chickens

Both pathogenic as well as nonpathogenic species of staphylococci have been reported in poultry, but these studies have not compared staphylococcal flora of both farmed and household broiler chickens. Staphylococci from farmed (n = 51) and household chicken intestines (n = 43) were isolated and tested for resistance to antimicrobials, presence of resistance genes, and inhibitory activity against other bacteria; correlation of resistance phenotype and genotype was also evaluated. At least 12 staphylococcal species were identified; Staphylococcus carnosus subspecies carnosus was the predominant species from both sources. Most farmed chicken staphylococci were resistant to tigecycline (38/51; 74.8%) while the highest level of resistance among the household chicken staphylococci was to clindamycin (31/43; 72.1%). The mecA gene was only detected in staphylococci from household chickens, whereas ermC and tetK or tetM were found in staphylococci from both groups of birds. Multidrug resistance (resistance ≥ 2 antimicrobial classes) was observed in 88% of resistant staphylococci ranging from 2 to 8 classes and up to 10 antimicrobials. Isolates produced inhibitory activity against 7 clinical bacterial strains primarily Enterococcus faecalis (25/88; 28.4%) and Escherichia coli (22/88; 25%). This study demonstrated that the staphylococcal population among farmed and household chickens varies by species and resistance to antimicrobials. These results may reflect the influence of the environment or habitat of each bird type on the intestinal microflora. As resistance in the staphylococci to antimicrobials used to treat human infections was detected, further study is warranted to determine strategies to prevent transfer of these resistant populations to humans via contamination of the poultry meat.

First report of mecC gene in clinical methicillin resistant S. aureus (MRSA) from tertiary care hospital Islamabad, Pakistan

BACKGROUND

Staphylococcus aureus (S. aureus) is one of the leading causes of community and hospital acquired infections globally. The objective of the study was to assess the prevalence, study the carriage of antibiotic resistance genes and evaluate the molecular typing of S. aureus isolates from a tertiary care hospital in Islamabad.

METHODS

A total of 1528 staphylococci isolates were included in this study. Standard microbiological procedures were applied to identify S. aureus. Antimicrobial susceptability was evaluated using the disk diffusion method and Minimum Inhibitory Concentrations (MICs) were determined using microbroth dilution method following Clinical and Laboratory Standards Institute (CLSI) guidelines. Multiplex PCR was used to detect antibiotic resistance genes, and molecular typing was performed using agr, SCCmec, spa, and Multi-Locus Sequence Typing (MLST) and clonal relatedness by Pulse Field Gel Electrophoresis (PFGE) methods.

RESULTS

Overall 65% were MRSA and 35% were methicillin sensitive Staphylococcus aureus (MSSA). Among MRSA isolates, 83% were multi-drug resistant and mecA was found in 54% isolates, mecC was in 3% while 1 MRSA carried both mecA and mecC genes. agrI (22%) was most prevalent group in MRSA, while agrIII (16%) was observed in MSSA. SCCmec types I, II, III, IV, and VI were detected, with high prevalence of type III while type V was absent. The prevelant spa type in MRSA was t657 with SCCmecIII elelments while in MSSA it was t021. One NEW spa type identified in MSSA isolates. In a subset of isolates, ST772 with SCCmecIV, ST1 carrying PVL marker, and ST1535 was reported first time from Pakistan.

CONCLUSIONS

The study presents a comprehensive analysis of prevalent S. aureus types and their antibiotic resistance profiles. It also reports for the first time SCCmec type VI and clinical MRSA isolates with mecC alone and in combination with mecA from Islamabad, Pakistan. This calls for further detailed investigations in other hospital settings in the region.

Antimicrobial resistance genes in bacteria from animal-based foods

Antimicrobial resistance is a worldwide public health threat. Farm animals are important sources of bacteria containing antimicrobial resistance genes (ARGs). Although the use of antimicrobials in aquaculture and livestock has been reduced in several countries, these compounds are still routinely applied in animal production, and contribute to ARGs emergence and spread among bacteria. ARGs are transmitted to humans mainly through the consumption of products of animal origin (PAO). Bacteria can present intrinsic resistance, and once antimicrobials are administered, this resistance may be selected and multiply. The exchange of genetic material is another mechanism used by bacteria to acquire resistance. Some of the main ARGs found in bacteria present in PAO are the bla, mcr-1, cfr and tet genes, which are directly associated to antibiotic resistance in the human clinic.

Detection and Molecular Characterization of Staphylococci from Eggs of Household Chickens

Eggs are a healthy and nutritious food source, but may be contaminated by bacteria. Previous studies have reported the presence of staphylococci in eggs of farmed chickens, but no study has evaluated the staphylococcal population of eggs from household chickens. In this study, staphylococci from eggs (n = 275) of household chickens collected from November 2016 to March 2017 from different villages of Khyber Pakhtunkhwa province, Pakistan, were characterized. Seven species of staphylococci were identified from 65 eggs, including the predominant species, Staphylococcus xylosus (49/275; 17.8%). S. xylosus isolates (n = 73) were tested for antimicrobial susceptibility, presence of resistance genes, genetic relatedness, and inhibitory activity against other bacteria. The majority of isolates were resistant to oxacillin (83.6%) and tetracycline (24.7%), but also exhibited resistance to daptomycin and linezolid (5.5% each). Of the 10 resistance genes tested, isolates were only positive for mecA (35.6%; 26/73), mecC/C1 (2.7%; 2/73), and tet(K) (14/73; 19%). Using pulsed-field gel electrophoresis (PFGE), nine clusters had identical PFGE patterns. Isolates produced inhibitory activity against a broad spectrum of bacteria; 20.5%, 19.2%, 17.8%, and 16.4% of S. xylosus were able to inhibit growth of Salmonella enterica serotype Typhi, methicillin-susceptible Staphylococcus aureus, Escherichia coli, and methicillin-resistant Staphylococcus aureus, respectively. This study demonstrated the presence of genetically related antimicrobial-resistant S. xylosus from eggs from household chickens. Like table eggs, eggs of household chickens also contain staphylococci that may be resistant to antimicrobials used to treat human infections. These data will allow comparison between staphylococci from eggs from different sources and may indicate the relative safety of eggs from household chickens. Further study of these egg types and their microbial composition is warranted.

Characterization of Staphylococcus aureus isolated from chicken and quail eggshell

Objectives:

This study was conducted to assess the prevalence and characterization of Staphylococcus aureus from chicken and quail eggshells and to study the antibiogram of the isolates.

Materials and methods:

A total of 300 eggs (220 chicken eggs and 80 quail eggs) were collected from different retail shops and farms in Mymensingh district. Swabs taken from the egg surfaces were cultured on Mannitol Salt Agar for the isolation of S. aureus. Polymerase chain reaction was conducted for confirmatory identification of the bacterial species targeting nuc gene, followed by confirmation of methicillin-resistant S. aureus by targeting the mecA gene. Antibiotic sensitivity test of the isolated bacteria was done against commonly used antibiotics by the disk diffusion method.

Results:

The prevalence of Staphylococcus spp. and S. aureus in the chicken eggshell surface was 20.45% and 10.45%, respectively. Similarly, the prevalence of Staphylococcus spp. and S. aureus in quail eggshell surface was 16.25% and 5%, respectively. Overall, 27 isolates were identified as S. aureus, of which 23 were from the chicken eggshell surface and four from quail eggshell surface. Among the seven isolates tested, overall four (57.14%) were positive for the nuc gene. On the other hand, the mecA gene could be detected in three (50%) S. aureus out of six oxacillin resistant isolates. The antibiogram study indicated that most of the isolates were resistant to the antibiotics under β-lactam group.

Conclusion:

The present study concludes that chicken and quail egg surface harbor multidrug-resistant bacteria which may cause public health hazards, if these antibiotic-resistant bacteria are transferred to a human.

LAB Bacteriocins Controlling the Food Isolated (Drug-Resistant) Staphylococci

Staphylococci are a group of microorganisms that can be often found in processed food and they might pose a risk for human health. In this study we have determined the content of staphylococci in 7 different fresh goat-milk cheeses. These bacteria were present in all of them, ranging from 103 to 106 CFU/g based on growth on selective media. Thus, a set of 97 colonies was randomly picked for phenotypic and genotypic identification. They could be clustered by RAPD-PCR in 10 genotypes, which were assigned by 16S rDNA sequencing to four Staphylococcus species: Staphylococcus aureus, Staphylococcus chromogenes, S. simulans, and S. xylosus. Representative strains of these species (n = 25) were tested for antibiotic sensitivity, and 11 of them were resistant to at least one of the antibiotics tested, including erythromycin, amoxicillin-clavulanic acid and oxacillin. We also tested two bacteriocins produced by lactic acid bacteria (LAB), namely the circular bacteriocin AS-48 and the lantibiotic nisin. These peptides have different mechanism of action at the membrane level. Nevertheless, both were able to inhibit staphylococci growth at low concentrations ranging between 0.16-0.73 μM for AS-48 and 0.02-0.23 μM for nisin, including the strains that displayed antibiotic resistance. The combined effect of these bacteriocins were tested and the fractional inhibitory concentration index (FICI) was calculated. Remarkably, upon combination, they were active at the low micromolar range with a significant reduction of the minimal inhibitory concentration. Our data confirms synergistic effect, either total or partial, between AS-48 and nisin for the control of staphylococci and including antibiotic resistant strains. Collectively, these results indicate that the combined use of AS-48 and nisin could help controlling (pathogenic) staphylococci in food processing and preventing antibiotic-resistant strains reaching the consumer in the final products.