First Case Report on Quantification of Antimicrobial Use in Corporate Dairy Farms in Pakistan

A systematic review and meta-analysis of carbapenem resistance and its possible treatment options with focus on clinical Enterobacteriaceae: Thirty years of development in Pakistan

Background

Carbapenem resistance is epidemic worldwide, these last resort antimicrobials are listed in the WHO 'watch group' with higher resistance potential. During the years 2017-18 Pakistan Antimicrobial Resistance Surveillance System reported an increase in carbapenem resistance. However, a comprehensive information on prevalence and molecular epidemiology of carbapenem resistance in Pakistan is not available. This systematic review and meta-analysis is aimed to report the current carbapenem resistance situation in Pakistan and its treatment options.

Methods

In this systematic review and meta-analysis, we investigated the pooled prevalence (PPr) of carbapenem resistance in Enterobacteriaceae and non-Enterobacteriaceae by organizing available data, from Web of Science and PubMed by April 2, 2020, in various groups and subgroups including species, years, provinces, extended spectrum β-lactamase production, clinical presentation, carbapenemase and metallo-β-lactamase production, and New Delhi metallo-β-lactamase (NDM) prevalence. Literature review was updated for the studies publisehd by December 07, 2023. Moreover, we descriptively reviewed the molecular epidemiology of carbapenem resistance in Enterobacteriaceae and non-Enterobacteriaceae in Pakistan. Lastly, we statistically explored different treatment options available for carbapenem resistant infections. We used R package 'metafor' for performing meta-analysis and influence diagnostics and determining treatment options.

Results

From two academic databases Web of Science and PubMed we identified 343 studies. Eighty-eight studies were selected for the systematic review and meta-analysis. Seventy-four studies were selected for phenotypic analysis, 36 for genotypic analysis, and 31 for available treatment options. PPr-ID of 12% [0.12 (0.07, 0.16)] was observed for phenotypic carbapenem resistance in Enterobacteriaceae with more prevalence recorded in Klebsiella pneumoniae 24% [0.24 (0.05, 0.44)] followed by 9% [0.09 (-0.03, 0.20)] in Escherichia coli. During the last two decades we observed a striking increase in carbapenem resistance PPr i.e., from 0% [0.00 (-0.02, 0.03)] to 36% [0.36 (0.17, 0.56)]. blaNDM with PPr 15% [0.15 (0.06, 0.23)] in naive isolates was found to be the fundamental genetic determinant for carbapenem resistance in Enterobacteriaceae in Pakistan. Polymyxin B, colistin, tigecycline, and fosfomycin were identified as the suggested treatment options available for multidrug resistant infections not responding to carbapenems. Various studies reported carbapenem resistance from human, animal, and environment sources.

Conclusion

In conclusion, we found that NDM-1 producing carbapenem resistant Enterobacteriaceae are increasing in Pakistan. Meta-analysis showed that metallo-β-lactamases producing E. coli ST405 and K. pneumoniae sequence type11 are the major resistant clones. Number of reported studies in various subgroups and inconsistency in following CLSI guidelines are the potential limitations of this meta-analysis. A National antimicrobial resistance (AMR) surveillance strategy based on One Health is urgently needed to check any future AMR crisis in Pakistan.

Assessment of the Implementation of Pakistan's National Action Plan on Antimicrobial Resistance in the Agriculture and Food Sectors

The agriculture and food (agrifood) sectors play key roles in the emergence, spread, and containment of antimicrobial resistance (AMR). Pakistan's first National Action Plan (NAP) on AMR was developed to guide One Health interventions to combat AMR through 2017-2022. To improve subsequent iterations, we assessed the implementation of Pakistan's NAP in the agrifood sectors (NAPag) in October 2022, using the Progressive Management Pathway on AMR tool developed by the Food and Agriculture Organization of the United Nations (FAO). The assessment tool addressed four crucial focus areas of the NAPag: governance, awareness, evidence, and practices. Each focus area contains multiple topics, which involve four sequential stages of activities to progressively achieve systematic management of AMR risk in the agrifood sectors. High-level representatives of the NAPag stakeholders provided information for the assessment through pre-event documentary review and workshop discussions. The assessment results showed that Pakistan's NAPag had an overall moderate coverage (59%) of the anticipated activities. Gaps were particularly notable in strengthening governance, good practices, and interventions in non-livestock sectors. Furthermore, only 12% of the evaluated activities were fully executed and documented, consistently remaining at the planning and piloting stages in the livestock sector across all the examined topics. Insufficient attention to non-livestock sectors, inadequate regulation and enforcement capacity, and resource constraints have hindered scalable and sustainable interventions under the current plan. This assessment provides valuable insights to strengthen the inclusiveness and contribution of the agrifood sectors in the next NAP iteration. In the short-to-medium term, strategic prioritization is necessary to optimize the use of limited resources and target the most critical gaps, such as improving awareness among key stakeholders and fortifying regulations for prudent antimicrobial use. In the long term, integration of AMR into the country's broader health, development, and agricultural transformation agendas will be needed to generate sustainable benefits.

Practices and drivers for antibiotic use in cattle production systems in Kenya

Understanding antibiotic use in livestock systems is key in combating antimicrobial resistance (AMR) and developing effective interventions. Using a standardised questionnaire, we investigated the patterns and drivers of antibiotic use in 165 cattle farms across the three major cattle production systems in Kenya: intensive, extensive, and semi-intensive systems across in three counties: Machakos, Makueni and Narok in Kenya. We used a causal diagram to inform regression models to explore the drivers of antibiotic use in the study farms. Antibiotic use was reported in 92.7% of farms, primarily for prophylactic purposes. Oxytetracycline, penicillin, and streptomycin were the most used antibiotics to treat and control the most reported diseases including mastitis, diarrhoea and East Coast fever (ECF). Regression analysis indicated a positive association between the frequency of antibiotic use at the farm level and both disease incidence and herd size. Conversely, farms that provided cattle with appropriate housing were less likely to use antibiotics, and there was no difference in antibiotic use between those who consulted with veterinarians or sourced antibiotics directly from animal health providers. Our study highlights the complexities around understanding the interplay between practices and drivers of antibiotic use. It also underscores the necessity to enhance education regarding the appropriate usage of antibiotics among cattle farmers, encourage the adoption of proper herd management practices which may reduce disease burden, and reinforce veterinary services and supportive legislation to promote the prudent use of antimicrobials.

International manufacturing and trade in colistin, its implications in colistin resistance and One Health global policies: a microbiological, economic, and anthropological study

BACKGROUND

The emergence of colistin-resistant Enterobacterales is a global public health concern, yet colistin is still widely used in animals that are used for food as treatment, metaphylaxis, prophylaxis, and growth promotion. Herein, we investigate the effect of colistin-resistant Enterobacterales in Pakistan, global trade of colistin, colistin use at the farm level, and relevant socioeconomic factors.

METHODS

We conducted a microbiological, economic, and anthropological study of colistin-resistant Escherichia coli in humans, animals, and the environment and international trade and knowledge of colistin in Pakistan, Bangladesh, Nigeria, China, India, and Viet Nam. We collected backyard poultry cloacal swabs, commercial broiler cloacal swabs, cattle and buffalo rectal swabs, human rectal swabs, wild bird droppings, cattle and buffalo meat, sewage water, poultry flies, chicken meat, and canal water from 131 sites across Faisalabad, Pakistan, to be tested for mcr-1-positive and mcr-3-positive Escherichia coli. We recruited new patients admitted to Allied Hospital, Faisalabad, Pakistan, with abdominal pain and diarrhoea for rectal swabs. Patients with dysentery and those who were already on antibiotic treatment were excluded. Data for colistin trade between 2017 and 2020, including importation, manufacturing, and usage, were accessed from online databases and government sources in Pakistan, Bangladesh, and Nigeria. We recruited participants from poultry farms and veterinary drug stores in Pakistan and Nigeria to be interviewed using a structured questionnaire. International manufacturing, import, and export data; value analysis; and trade routes of colistin pharmaceutical raw material (PRM), feed additive, and finished pharmaceutical products (FPPs) were accessed from 2017-21 export data sets.

FINDINGS

We collected 1131 samples between May 12, 2018, and July 1, 2019: backyard poultry cloacal swabs (n=100), commercial broiler cloacal swabs (n=102), cattle and buffalo rectal swabs (n=188), human rectal swabs (n=200), wild bird droppings (n=100), cattle and buffalo meat (n=100), sewage water (n=90), poultry flies (n=100), chicken meat (n=100), and canal water (n=51). We recruited 200 inpatients at Allied Hospital, Faisalabad, Pakistan, between Nov 15, 2018, and Dec 14, 2018, for rectal swabs. We recruited 21 participants between Jan 1, 2020, and Dec 31, 2020, from poultry farms and drug stores in Pakistan and Nigeria to be interviewed. 75 (7%) of 1131 samples contained mcr-1-positive E coli, including wild bird droppings (25 [25%] of 100), commercial broiler cloacal swabs (17 [17%] of 100), backyard poultry cloacal swabs (one [1%] of 100), chicken meat (13 [13%] of 100), cattle and buffalo meat (two [2%] of 100), poultry flies (eight [8%] of 100), sewage water (six [7%] of 90), and human rectal swabs (three [2%] of 200). During 2017-20, Pakistan imported 275·5 tonnes (68·9 tonnes per year, 95% CI 41·2-96·6) of colistin as PRM, all sourced from China, 701·9 tonnes (175·5 tonnes per year, 140·9-210·1) of colistin as feed additives from China and Viet Nam, and 63·0 tonnes (15·8 tonnes per year, 10·4-21·1) of colistin as FPPs from various countries in Asia and Europe. For Bangladesh and Nigeria, colistin PRM and FPPs were imported from China and Europe. Colistin knowledge and usage practices in Pakistan and Nigeria were unsatisfactory in terms of understanding of the effects on human medicine and usage other than for treatment purposes. China is the major manufacturer of PRM and feed additive colistin and exported a total of 2664·8 tonnes (666·2 tonnes per year, 95% CI 262·1 to 1070·2) of PRM and 2570·2 tonnes (642·6 tonnes per year, -89·4 to 1374·5) of feed additive in 1330 shipments during 2018-21 to 21 countries.

INTERPRETATION

Regardless of 193 countries signing the UN agreement to tackle antimicrobial resistance, trading of colistin as PRM, FPPs, and feed additive or growth promoter in low-income and middle-income countries continues unabated. Robust national and international laws are urgently required to mitigate the international trade of this antimicrobial listed on WHO Critically Important Antimicrobials for Human Medicine.

FUNDING

Pakistan Agricultural Research Council and INEOS Oxford Institute for Antimicrobial Research TRANSLATION: For the Urdu translation of the abstract see Supplementary Materials section.

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.

Veterinary consumption of highest priority critically important antimicrobials and various growth promoters based on import data in Pakistan

Background

Antimicrobial resistance (AMR) is a global public health emergency driven by the indiscriminate use of antimicrobial agents in humans and animals. Antimicrobial consumption surveillance guides its containment efforts. In this study, we estimated, for the first time, veterinary consumption of Critically Important Antimicrobials with Highest Priority (CIA-HtP) for Pakistan.

Methods

The study used an export/import database which provided imports data collected from the Pakistan Customs Authority. We investigated imports of 7 CIA-HtP and various poultry feed additives/growth promoters (FAs/GPs) identified from a survey of 10 poultry and dairy farms in Punjab province in Pakistan and a previously published study, over a three-year period of 2017–2019. Antimicrobial consumption was estimated in mg/kg of country’s animal biomass.

Findings

Imports, in tonnes, for these 7 CIA-HtP were for the years 2017–19: tylosin 240.84, enrofloxacin 235.14, colistin 219.73, tilmicosin 97.32, spiramycin 5.79, norfloxacin 5.55, ceftiofur 1.02 for a total 805.39 tonnes. The corresponding antimicrobial consumption was 10.05 mg/kg of animal biomass. The poultry FAs/GPs contained: zinc bacitracin, enramycin, bacitracin methylene disalicylate, tylosin, tiamulin, colistin, lincomycin, streptomycin, flavophospholipol, tilmicosin, and penicillin with a total antimicrobial chemical compound (ACC) import volume of 577.18 tonnes for the years 2017–2019; and an estimated consumption of 96.53 mg/kg of poultry biomass.

Interpretation

These antimicrobials were a mix of macrolides, quinolones, polymyxins and cephalosporins, among which are some also on the Watch or Reserve list by the WHO, indicating the need for stewardship and to conserve essential antimicrobials to contain AMR. The finding that a yearly average of 192.39 tonnes of the ACC imported were FAs/GPs further highlight the need for stronger regulation and enforcement.

Evaluating the antimicrobial use on dairy farms in Chiba Prefecture in Japan using the antimicrobial treatment incidence, an indicator based on Japanese defined daily doses from 2014-2016

The use of antimicrobial agents in food-producing animals may lead to the emergence and spread of antimicrobial resistance in bacteria of animal origin. However, there is a paucity of data on the quantity of antimicrobials use on dairy farms in Japan. This study describes antimicrobial use on dairy farms from 1 January 2014 to 31 December 2016 in five administrative districts (central, eastern, western, southern and northern) of Chiba Prefecture. The use of antimicrobial agents in dairy cattle over these three years was evaluated in terms of the antimicrobial treatment incidence (ATI; theoretical number of animals per 1,000 animal-days subjected to antimicrobial treatment) using data collected from a total of 442 dairy farms in that prefecture. Our results revealed that the average ATI on these farms for these years ranged from 38.7 to 39.4 with no significant difference between years and that the average ATI for these administrative districts varied between 32.9 and 43.2 with a significant variation between some of the districts. Approximately 84% of antimicrobials were administered intramammarily, 13–14% by injection and 1–2% orally. Scenario analyses were performed to assess the effect of changes in some of the defined daily dose (DDDjp) values used to calculate the ATI. Our results revealed that the calculated ATI is considerably affected by the changes in the long-acting factor used for assigning the DDDjp values of intramammary products for dry cows and the way in which DDD values are assigned for combination products.

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.

Emergence of plasmid-mediated tigecycline resistance tet(X4) gene in Escherichia coli isolated from poultry, food and the environment in South Asia

The recent emergence of mobile-tigecycline resistance tet(X) genes in human and animals in China seriously threats the clinical utility of tigecycline. Here we focused on the isolation and molecular characterization of plasmid-mediated tigecycline resistance tet(X4)-positive E. coli from different sources in Pakistan using MinION and Illumina sequencing. The tet(X4) gene was detected in four E. coli isolates from poultry, chicken meat, wild bird and the slaughterhouse wastewater in Pakistan. Co-existence of colistin resistance mcr-1 gene was also detected in three isolates. The four isolates belonged to different sequence types and the tet(X4) gene was located on plasmids ranging from 12,331 bp to 113,610 bp belonging to IncFII and IncQ replicon types with two genetic contexts ISCR2-tet(X4)-abh-ISCR2-lysR-floR-virD2 and ΔISCR2-abh-tet(X4)-ISCR2-virD2-floR, respectively. In all the four E. coli strains, tet(X4) was transferable by conjugation to E. coli J53 host strain. In addition, three of four strains transferred tet(X4) to a wild-type carbapenem resistant E. coli strain. To our knowledge, this is the first report of the emergence of plasmid-mediated tet(X4) gene from Pakistan. The convergence of tigecycline and colistin resistance in South Asia is a serious threat to human health.