DOI: 10.5061/dryad.hhmgqnkp7
title: Pathogen group-specific risk factors for intra-mammary infection in water buffalo

description: A cross-sectional study was conducted to estimate the prevalence of
 intra-mammary infection (IMI) associated bacteria and to identify risk
 factors for pathogen group-specific IMI in water buffalo in Bangladesh. A
 California Mastitis Test (CMT) and bacteriological cultures were performed
 on 1,374 quarter milk samples collected from 763 water buffalo from 244
 buffalo farms in nine districts in Bangladesh. Quarter, buffalo, and
 farm-related data were obtained through questionnaires and visual
 observations. A total of 618 quarter samples were found to be
 culture-positive. Non-aureus staphylococci were the predominant
 IMI-associated bacterial species, and Staphylococcus (S.) chromogenes, S.
 hyicus, and S. epidermidis were the most common bacteria found. The
 proportion of non-aureus staphylococci or Mammaliicoccus sciuri (NASM), S.
 aureus, and other bacterial species identified in the buffalo quarter
 samples varied between buffalo farms. Therefore, different management
 practices, buffalo breeding factors, and nutrition were considered and
 further analyzed when estimating the IMI odds ratio (OR). The odds of IMI
 by any pathogen (OR: 1.8) or by NASM (OR: 2.2) were high in buffalo herds
 with poor milking hygiene. Poor cleanliness of the hind quarters had a
 high odds of IMI caused by any pathogen (OR: 2.0) or NASM (OR: 1.9). Twice
 daily milking (OR: 3.1) and farms with buffalo purchased from another herd
 (OR: 2.0) were associated with IMI by any pathogen. Asymmetrical udders
 were associated with IMI-caused by any bacteria (OR: 1.7). A poor body
 condition score showed higher odds of IMI by any pathogen (OR: 1.4) or by
 NASM (OR: 1.7). This study shows that the prevalence of IMI in water
 buffalo was high and varied between farms. In accordance with the
 literature, our data highlight that IMI can be partly controlled through
 better farm management, primarily by improving hygiene, milking
 management, breeding, and nutrition.
description: The data was collected through a face-to-face interview with the
 farmer, and on-farm observations were taken. During the interview, the
 farmers gave information on the buffalo source, breed type, and frequency
 of milking per day. In contrast, animal information, such as body
 condition score (BCS), udder symmetry, udder shape, type of hand milking
 procedure, cleanliness of the hind quarter, and milking hygiene, was
 assessed through on-farm observations by the interviewer. Data analysis
 was done using R statistical software (version 4.1.2; R Foundation for
 Statistical Computing, Vienna, Austria). The prevalence of IMI in healthy
 (CMT = 1) or SCM quarter (CMT ≥ 2) samples was calculated by dividing the
 number of samples positive for each bacterial species (NASM; <em>S.
 aureus</em>; <em>Streptococcus</em>; Gram-negative; or
 other bacteria) by the total number of tested quarter milk samples. The
 exact binomial method was used to calculate the proportion's 95%
 confidence intervals. The prevalence of IMI-associated bacterial species
 was calculated at the quarter, animal, and farm levels. Mixed-effects
 logistic regression models with animal and farm ID as random effects were
 constructed to test the association between IMI-associated bacterial
 species and buffalo or farm-level variables. The significance of the
 random effect terms was checked using a Likelihood Ratio Test (LRT) using
 the latent variable approach [24]. Variables for which the univariable
 <em>P</em> value was &lt; 0.20 were included in the
 multivariable model. The multivariable model was built using a stepwise
 forward selection procedure, adding each significant variable in the
 model, starting with the variable with the lowest <em>P</em>
 value. Finally, the association of significant (<em>P</em> ≤
 0.05) variables with the outcome was presented in terms of
 subject-specific odds ratios (OR) and 95% CI.
description: # Pathogen group-specific risk factors for intra-mammary infection in
 water buffalo 1. Author Information A. Principal Investigator Contact
 Information Name: Prof. Dr. Md. Mizanur Rahman Institution: Department of
 Medicine and Surgery, Chattogram Veterinary and Animal Sciences University
 Address: Zakir Hossain Road, Khulshi, Chattogram, Bangladesh Email:
 [mizanuhcp@cvasu.ac.bd](mailto:mizanuhcp@cvasu.ac.bd) B. Associate or
 Co-investigator Contact Information Name: Ylva Persson Institution:
 Department of Clinical Sciences, Swedish University of Agricultural
 Sciences Address: Uppsala, Sweden Email:
 [ylva.persson@sva.se](mailto:ylva.persson@sva.se) 2. Date of data
 collection: 2020-2021 3. The geographic location of data collection:
 Rajshahi, Jamalpur, Mymensingh, Moulvibazar, Bhola, Laxmipur, Dhaka,
 Noakhali, and Chattogram district of Bangladesh ## SHARING/ACCESS
 INFORMATION Recommended citation for this dataset: Singha, Shuvo; Rahman,
 Md. Mizanur; Persson, Ylva (Forthcoming 2024). Pathogen group-specific
 risk factors for intramammary infection in water buffalo [Dataset]. Dryad.
 [https://doi.org/10.5061/dryad.hhmgqnkp7](https://doi.org/10.5061/dryad.hhmgqnkp7) ## DATA & FILE OVERVIEW File List: 1. Proportion_of_IMI_animal.xlsx 2. Proportion_of_IMI_farm.xlsx 3. SCM_pathogens.xlsx 4. Pathogens by farms.xlsx 5. Proportion_of_pathogens.xlsx ### DATA-SPECIFIC INFORMATION FOR: A.\_Proportion\_of\_IMI\_animal.xlsx Number of variables: 10 Number of cases/rows: 764 Variable List: * AID: Animal identification number * Any_pathogen: Binary variable (Yes/No); 1=Culture positive for any of this pathogen NAS/*Mammaliicoccus*/Gram_neg/Other_bac/*Staph_au*/Not_iden/Strept; 0=Culture negative * NAS: Binary variable (Yes/No); 1=Culture positive for Non-*aureus* staphylococci (NAS) 0=Culture negative for NAS *Mammaliicoccus* Binary variable (Yes/No); 1=Culture positive for *Mammaliicoccus* 0=Culture negative for *Mammaliicoccus* spp * Gram_neg: Binary variable (Yes/No); 1=Culture positive for Gram Negative bacteria 0=Culture negative for Gram Negative bacteria * Other_bac: Binary variable (Yes/No); 1=Culture positive for Other bacteria 0=Culture negative for Other bacteria * Staph_au: Binary variable (Yes/No); 1=Culture positive for *Staphylococcus aureus* 0=Culture negative for *Staphylococcus aureus* * Not_iden: Binary variable (Yes/No); 1=Culture positive for Non-identifiable bacteria by MALDI-TOF 0=Culture negative for Non-identifiable bacteria by MALDI-TOF * Strept: Binary variable (Yes/No); 1=Culture positive for *Streptococcus* spp 0=Culture negative for *Streptococcus* spp * SCMType_AID: Subclinical mastitis (SCM) at the animal level (Yes/No); 1= At least one quarter is positive for SCM; 0= All quarers are negative for SCM ### DATA-SPECIFIC INFORMATION FOR: B.\_Proportion\_of\_IMI\_farm.xlsx Number of variables: 10 Number of cases/rows: 245 Variable List: * FID: Farm identification number * Any_pathogen: Binary variable (Yes/No); 1=Culture positive for any of this pathogen NAS/*Mammaliicoccus*/Gram_neg/Other_bac/*Staph_au*/Not_iden/Strept; 0=Culture negative * NAS: Binary variable (Yes/No); 1=Culture positive for Non-*aureus* staphylococci (NAS) 0=Culture negative for NAS *Mammaliicoccus* Binary variable (Yes/No); 1=Culture positive for *Mammaliicoccus* 0=Culture negative for *Mammaliicoccus* spp * Gram_neg: Binary variable (Yes/No); 1=Culture positive for Gram Negative bacteria 0=Culture negative for Gram Negative bacteria * Other_bac: Binary variable (Yes/No); 1=Culture positive for Other bacteria 0=Culture negative for Other bacteria * Mammaliicoccus: Binary variable (Yes/No); 1=Culture positive for *Mammaliicoccus* 0=Culture negative for *Mammaliicoccus* spp * Staph_au: Binary variable (Yes/No); 1=Culture positive for *Staphylococcus aureus* 0=Culture negative for *Staphylococcus aureus* * Not_iden: Binary variable (Yes/No); 1=Culture positive for Non-identifiable bacteria by MALDI-TOF 0=Culture negative for Non-identifiable bacteria by MALDI-TOF * Strept: Binary variable (Yes/No); 1=Culture positive for *Streptococcus* spp 0=Culture negative for *Streptococcus* spp * SCMType_FID: Subclinical mastitis (SCM) at the farm level (Yes/No); 1= At least one animal is positive for SCM; 0= All animal are negative for SCM ### DATA-SPECIFIC INFORMATION FOR: C.\_SCM\_pathogens.xlsx Number of variables: 67 Number of cases/rows: 1375 Variable List: * N ID: Continuous serial number to enable sorting and filtering option in Excel * Visit name: Name of sampling regions * Quarter ID_original: Original identification number for the individual quarters * SCM Type: Subclinical mastitis status * AID: Animal Identification Number Pathogen data from quarter samples: * Culture_negative: 1=Yes; 0=No * NAS: Non-*aureus staphylococcus*; 1=Yes; 0=No * Mammaliicoccus: 1=Yes; 0=No * Gram_neg: Gram Negative; 1=Yes; 0=No * Other_bac: Other Bacteria; 1=Yes; 0=No * Staph_au: *Staph. aureus*; 1=Yes; 0=No * Not_iden: Not identified by MALDI-TOF; 1=Yes; 0=No * Strept: *Streptococcus*; 1=Yes; 0=No * CMT score: California mastitis test score 1 to 5; 1=No mastitis or Healthy 2/3/4/5=Subclinical mastitis * Bacterial growth: Status of microorganisms identification Quarter data * Quarter ID: Orignal quarter ID from raw questionnaire sheet * QP: Teat position; FL=Front left; FR=Front right; HL=Hind left; HR=Hind right * QP_RL: Right/ Left teat position; Front right/ Hind right=Right; Front left/Hind left=Left * QP_FH: Front/ Hind teat position; Front left/ Front right= Front; Hind left/ Hind right= Hind * T_shape: Teat shape; 1=Funnel shape; 2=Bottle shape; 3=Cylindrical shape * T_lesion: Presence of any teat lesions (Injury/ teat disease lesions); 1=Yes; 0=No * T_congenital: Presence of any teat congenital lesions; 1=Yes; 0=No Animal data * AID: Continuous Animal identification number (For use as random effects during analysis) * AID_original: Orignal animal ID from raw questionnaire sheet * B_mastitis: Mastitis at buffalo level (If one quarter is positive=animal is positive; if all quarters are negative=animal is healthy); 1=Subclinical mastitis; 0=Healthy * Age: Age of the buffalo in years; data taken according to farmers idea * Breed: Buffalo breeds * BCS: Body condition score; Score 1 to Score 9 * A_my: Average milk yield in litres per day * L_stage: Number of months in milk; data taken according to farmers idea * Pregnancy: Pregnancy status of the buffalo; 1=Pregnant; 2=Non-pregnant * Parity: Number of calves given birth; data taken according to farmers idea * U_symmetry: Udder symmetry; 1=Symmetric; 2=Asymmetric * U_shape: Udder shape; 1=Cup/Pendulous; 2=Round/Globular; 3=Bowl * T_block: If the animal has no milk in any quarter due to previous mastitis or any other reason; 1=Yes; 0=No * T_congenital: If the animal has any congenital anomalies in any of the quarters; 1=Yes; 0=No * T_position: Position of teats of the animal; 1=Symmetrical; 2=Directed backward; 3=Directed inward; 4=Directed outward; 5=Others * C_hind_quarter: Cleanliness of the hind quarter of the animal (Data taken one-time observation during milking); 1=Excellent; 2=Good; 3=Poor * U_dis: Any previous history of udder-related disease in the previous 12 months; 1=Yes; 0=No * H_any_dis: Any previous history of other diseases in the previous 12 months; 1=Yes; 0=No * H_lameness: Any previous history of lameness in the previous 12 months; 1=Yes; 0=No * H_cm: Any previous history of clinical mastitis signs observed in the previous 12 months; 1=Yes; 0=No * H_abort: Any previous history of abortion observed in the previous 12 months; 1=Yes; 0=No * H_calf_m: Any previous history of calf mortality observed in the previous 12 months; 1=Yes; 0=No Farm data * FID_original: Orignal farm ID from raw questionnaire sheet * FID: Continuous farm identification number (For use as random effects during analysis) * BMSCC: Bulk milk somatic cell count from the composite milk of all the lactating buffaloes in a herd * Log10BMSCC: Log10 transformation of BMSCC data to normalize * R_system: Buffalo rearing systems * Month: Month of sampling * Education: Education level of the farmer; 0=Illiterate; 1=Primary; 2=Secondary; 3=Graduation * TN_Buffalo: Total number of buffaloes in the herd * N_lactating: Total number of lactating buffaloes in the herd * Breeds: Type of buffalo breeds in the herd * Feeding_S: Type of buffalo feeding system; 0=Stall feeding; 1=Grazing; 2=Both * B_source: Source of buffaloes in the herd; 0=Own stock; 1=Purchased; 2=Both 3=Take care other's buffaloes * Wash_buffalo: If the farmer washes the buffaloes as a regular practice before milking; 0=No; 1=Yes * Control_milk: If the farmer tethers the buffaloes to physical restrain before milking; 0=No; 1=Yes * Wash_udder: If the farmer washes the buffalo udder as a regular practice before milking; 0=No; 1=Yes * Dry_udder: If the farmer dries the buffalo udder as a regular practice before milking; 0=No; 1=Yes * T_dipping: If teat dipping is applied before milking; 0=No; 1=Yes * T_hand_milk: Type of hand milking practiced; 1=Full hand; 2=Stripping; 3=Knuckling * Fre_milking: Frequency of milking * Udder_hygiene: Scoring of udder hygiene; 1=Excellent (Washing udder+pre/post-dip, dry udder); 2=Good (Washing udder+dip); 3=Fair (Washing udder); 4=Poor (Nothing) * Milker_hygiene: Scoring of milker hygiene; 1=Excellent (Antiseptic+Hand wash); 2=Good (Only hand wash); 3=Poor (Never wash hands) * N_milker: Number of milker do the milking in the herd; 0=Same person; 1=Multiple milker * Milk_cm_last: If the farmer milks the clinical mastitis-affected buffalo at last; 0=No; 1=Yes * Blank cells: data not available ### DATA-SPECIFIC INFORMATION FOR: D\_Pathogens by farms.xlsx Number of variables: 11 Number of cases/rows: 1331 Variable List: * QID: Quarter identification number * FID: Farm identification number * AID: Animal identification number * Type of bacteria: Categorical variable; Culture negative; Gram negative; NAS; Other bacteria; *S. aureus*; *Streptococcus* * NAS: Binary variable (Yes/No); 1=Culture positive for Non-*aureus* staphylococci (NAS) 0=Culture negative for NAS * S. aureus: Binary variable (Yes/No); 1=Culture positive for *Staphylococcus aureus* 0=Culture negative for *Staphylococcus aureus* * Streptococcus: Binary variable (Yes/No); 1=Culture positive for *Streptococcus* spp 0=Culture negative for *Streptococcus* spp * Gram negative: Binary variable (Yes/No); 1=Culture positive for Gram Negative bacteria 0=Culture negative for Gram Negative bacteria * Other bacteria: Binary variable (Yes/No); 1=Culture positive for Other bacteria 0=Culture negative for Other bacteria * SCM: Subclinical mastitis (SCM) at the quarter level (Yes/No); 1= If the quarter is positive for SCM; 0= If the quarter is negative for SCM * CMT score: California mastitis test score 1 to 5; 1: Negative; 2: Suspicious quarter; 3: Mild; 4: Moderate; 5: Severe * F = female * M = male * U = unknown * UF = unknown but suspected female * UM = unknown but suspected male ### DATA-SPECIFIC INFORMATION FOR: E. Proportion\_of\_pathogens.xlsx Number of variables: 10 Number of cases/rows: 245 Variable List: * FID: Farm identification number * AP_%: Farm-level prevalence for any pathogen; NAS/*Mammaliicoccus*/Gram_neg/Other_bac/*Staph_au*/Not_iden/Strept; 0=Culture negative * GN_%: Farm-level prevalence for Gram Negative bacteria * OB_%: Farm-level prevalence for Other bacteria * Strep_%: Farm-level prevalence for *Streptococcus* spp * NI_%: Farm-level prevalence for Non-identifiable bacteria * NASM(%): Farm-level prevalence for Non-*aureus* *Staphylococcus* or *Mammaliicoccus* * SA_%: Farm-level prevalence for *Mammaliicoccus* * CN_%: Farm-level prevalence for Culture negative * NA: data not available